Merge pull request datashield#553 from StuartWheater/v6.3.1-RC5-dev

Updates from RC5

Author: StuartWheater

.Rbuildignore

@@ -19,4 +19,6 @@
 ^docs$
 ^dsBase_6.3.1.tar.gz$
 ^dsBase_6.3.1-permissive.tar.gz$
-^dsDanger_6.3.0.tar.gz$
+^dsDanger_6.3.1.tar.gz$
+^\.circleci$
+^\.circleci/config\.yml$

.circleci/config.yml

@@ -0,0 +1,51 @@
+# Copyright (c) 2024 Arjuna Technologies, Newcastle upon Tyne. All rights reserved.
+
+version: 2.1
+
+jobs:
+  dsbaseclient:
+    docker:
+      - image: cimg/base:current
+    resource_class: small
+    steps:
+      - checkout
+      - setup_remote_docker:
+          docker_layout_caching: true
+      - run: |
+          echo "Building"
+          echo "  Repo Name: " $CIRCLE_PROJECT_REPONAME
+          echo "  Branch:    " $CIRCLE_BRANCH
+          echo "  Tag:       " $CIRCLE_TAG
+      - run:
+          command: |
+              sudo apt-get update -y
+              sudo apt-get install -y r-base-core cmake
+      - run:
+          command: |
+              sudo apt-get install -y libxml2-dev
+              sudo apt-get install -y libfontconfig1-dev
+              sudo apt-get install -y libudunits2-dev
+              sudo apt-get install -y libharfbuzz-dev
+              sudo apt-get install -y libfribidi-dev
+              sudo apt-get install -y libfreetype6-dev
+              sudo apt-get install -y libpng-dev
+              sudo apt-get install -y libtiff5-dev
+              sudo apt-get install -y libjpeg-dev
+      - run:
+          command: |
+              sudo Rscript -e "install.packages('fields', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('metafor', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('meta', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('ggplot2', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('gridExtra', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('data.table', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('panelaggregation', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('methods', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('dplyr', dependencies=TRUE)"
+      - run:
+          command: |
+              sudo Rscript -e 'library(covr); covr::codecov(token = "'$CODECOV_TOKEN'", quiet=FALSE)'
+workflows:
+  build:
+    jobs:
+      - dsbaseclient

DESCRIPTION

@@ -1,13 +1,13 @@
 Package: dsBaseClient
 Title: DataSHIELD Client Functions
-Version: 6.3.1.9000
+Version: 6.3.1
 Author: DataSHIELD Developers <datashield@liverpool.ac.uk>
 Maintainer: DataSHIELD Developers <datashield@liverpool.ac.uk>
 Description: DataSHIELD client functions for the client side.
 License: GPL-3
 Depends:
-    R (>= 3.5.0),
-    DSI (>= 1.3.0)
+    R (>= 4.0.0),
+    DSI (>= 1.7.1)
 Imports:
     fields,
     metafor,
@@ -20,5 +20,5 @@ Imports:
     dplyr
 Suggests:
     testthat
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Encoding: UTF-8

R/ds.glm.R

@@ -63,7 +63,7 @@
 #' The \code{data} argument avoids you having to specify the name of the
 #' data frame in front of each covariate in the formula. 
 #' For example, if the data frame is called \code{DataFrame} you
-#' avoid having to write: \eqn{DataFrame$y~DataFrame$a+DataFrame$b+DataFrame$c+DataFrame$d}
+#' avoid having to write: \eqn{DataFrame\$y ~ DataFrame\$a + DataFrame\$b + DataFrame\$c + DataFrame\$d}
 #' 
 #' The \code{checks} argument verifies that the variables in the model are all defined (exist) 
 #' on the server-side at every study

R/ds.glmSLMA.R

@@ -134,7 +134,7 @@
 #' The \code{dataName} argument avoids you having to specify the name of the
 #' data frame in front of each covariate in the formula. 
 #' For example, if the data frame is called \code{DataFrame} you
-#' avoid having to write: \eqn{DataFrame$y~DataFrame$a+DataFrame$b+DataFrame$c+DataFrame$d}
+#' avoid having to write: \eqn{DataFrame\$y ~ DataFrame\$a + DataFrame\$b + DataFrame\$c + DataFrame\$d}
 #' 
 #' The \code{checks} argument verifies that the variables in the model are all defined (exist) 
 #' on the server-site at every study

R/ds.glmerSLMA.R

@@ -34,7 +34,7 @@
 #' The \code{dataName} argument avoids you having to specify the name of the
 #' data frame in front of each covariate in the formula. 
 #' For example, if the data frame is called \code{DataFrame} you avoid having to write: 
-#' \eqn{DataFrame$y~DataFrame$a+DataFrame$b+(1|DataFrame$c)}.
+#' \eqn{DataFrame\$y ~ DataFrame\$a + DataFrame\$b + (1 | DataFrame\$c)}.
 #' 
 #' The \code{checks} argument verifies that the variables in the model are all defined (exist) 
 #' on the server-site at every study

R/ds.lmerSLMA.R

@@ -18,20 +18,20 @@
 #' 
 #' In \code{formula} most shortcut notation allowed by  \code{lmer()} function is
 #' also allowed by \code{ds.lmerSLMA}. Many LMEs can be fitted very simply using a formula like:
-#' \deqn{y~a+b+(1|c)}
+#' \deqn{y ~ a + b + (1 | c)}
 #' which simply means fit an LME with \code{y} as the outcome variable with \code{a} and \code{b}
 #' as fixed effects, and \code{c} as a random effect or grouping factor.
 #' 
 #' It is also possible to fit models with random slopes by specifying a model such as 
-#' \deqn{y~a+b+(1+b|c)} 
+#' \deqn{y ~ a + b + (1 + b | c)}
 #' where the effect of \code{b} can vary randomly between groups defined by \code{c}.
-#' Implicit nesting can be specified with formulae such as \eqn{y~a+b+(1|c/d)}
-#' or \eqn{y~a+b+(1|c)+(1|c:d)}. 
+#' Implicit nesting can be specified with formulae such as \eqn{y ~ a + b + (1 | c / d)}
+#' or \eqn{y ~ a + b + (1 | c) + (1 | c : d)}.
 #' 
 #' The \code{dataName} argument avoids you having to specify the name of the
 #' data frame in front of each covariate in the formula. 
 #' For example, if the data frame is called \code{DataFrame} you avoid having to write: 
-#' \eqn{DataFrame$y~DataFrame$a+DataFrame$b+(1|DataFrame$c)}.
+#' \eqn{DataFrame\$y ~ DataFrame\$a + DataFrame\$b + (1 | DataFrame\$c)}.
 #' 
 #' The \code{checks} argument verifies that the variables in the model are all defined (exist) 
 #' on the server-site at every study
@@ -192,7 +192,7 @@
 #'  
 #'   # Fit the lmer
 #'   
-#'   ds.lmerSLMA(formula = "BMI ~  incid_rate + diabetes + (1 | Male)",
+#'   ds.lmerSLMA(formula = "BMI ~ incid_rate + diabetes + (1 | Male)",
 #'                dataName = "D.comp",
 #'                datasources = connections)
 #'   

README.md

@@ -3,16 +3,6 @@ dsBaseClient
 
 DataSHIELD client side base R library.
 
-| Branch   | dsBase status | dsBase tests | dsBaseClient status | dsBaseClient tests |
-| -------- | ------------- | ------------ | ------------------- | ------------------ |
-| Master   | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBase?branchName=master)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=3&branchName=master) | | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBaseClient?branchName=master)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=master) | [Tests](https://datashield.github.io/testStatus/dsBaseClient/master/latest/) |
-| 6.0 | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBase?branchName=v6.0)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=3&branchName=v6.0) | | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBaseClient?branchName=v6.0)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=v6.0) | [Tests](https://datashield.github.io/testStatus/dsBaseClient/v6.0/latest/) |
-| 6.0.1 | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBase?branchName=v6.0.1)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=3&branchName=v6.0.1) | | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBaseClient?branchName=v6.0.1)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=v6.0.1) | [Tests](https://datashield.github.io/testStatus/dsBaseClient/v6.0.1/latest/) |
-| 6.1 | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBase?branchName=v6.1)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=3&branchName=v6.1) | [Tests](https://datashield.github.io/testStatus/dsBase/v6.1/latest/) | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBaseClient?branchName=v6.1)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=v6.1) | [Tests](https://datashield.github.io/testStatus/dsBaseClient/v6.1/latest/) |
-| 6.1.1 | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBase?branchName=v6.1.1)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=3&branchName=v6.1.1) | [Tests](https://datashield.github.io/testStatus/dsBase/v6.1.1/latest/) | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBaseClient?branchName=v6.1.1)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=v6.1.1) | [Tests](https://datashield.github.io/testStatus/dsBaseClient/v6.1.1/latest/) |
-| 6.2 | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBase?branchName=v6.2)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=3&branchName=v6.2) | [Tests](https://datashield.github.io/testStatus/dsBase/v6.2/latest/) | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBaseClient?branchName=v6.2)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=v6.2) | [Tests](https://datashield.github.io/testStatus/dsBaseClient/v6.2/latest/) |
-
-
 [![License](https://img.shields.io/badge/license-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.html)
 
 About

armadillo_azure-pipelines.yml

@@ -71,7 +71,7 @@ jobs:
 - job: build_and_run_tests
   timeoutInMinutes: 360
   pool:
-    vmImage: ubuntu-22.04
+    vmImage: ubuntu-24.04
 
   steps:
     #####################################################################################
@@ -125,11 +125,11 @@ jobs:
     # Install R and all the dependencies dsBaseClient requires.
     # If previous steps have failed then don't run.
   - bash: |
-
-      sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
-      sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/"
-      sudo add-apt-repository ppa:cran/libgit2
-      sudo apt-get update
+      sudo apt-get install --no-install-recommends software-properties-common dirmngr
+      wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+      sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
+      sudo apt-get update -qq
+      sudo apt-get upgrade -y
 
       sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
       sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev -y
@@ -139,7 +139,7 @@ jobs:
       sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
       sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 
-      sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='v6.3.0-dev', dependencies = TRUE)"
+      sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)"
 
       # XML grep for coverage report merging
       sudo apt-get install -qq xml-twig-tools -y
@@ -273,7 +273,7 @@ jobs:
       # junit reporter output is to test_results.xml
       #
       # "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
-      # testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
+      # testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
       sudo R -q -e '
         library(covr);
         dsbase.res <- covr::package_coverage(
@@ -288,8 +288,9 @@ jobs:
                 junit_rep <- JunitReporter$new(file = "test_results_dsbase.xml");
                 progress_rep <- ProgressReporter$new(max_failures = 999999);
                 multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
+                options("datashield.return_errors" = FALSE);
                 options("default_driver" = "ArmadilloDriver");
-                testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
+                testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
                 '"'"'
             )
         );
@@ -409,6 +410,7 @@ jobs:
                 junit_rep <- JunitReporter$new(file = "test_results_dsdanger.xml");
                 progress_rep <- ProgressReporter$new(max_failures = 999999);
                 multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
+                options("datashield.return_errors" = FALSE);
                 options("default_driver" = "ArmadilloDriver");
                 testthat::test_package("$(projectName)", filter = "__dgr-|datachk_dgr-|smk_dgr-|arg_dgr-|disc_dgr-|smk_expt_dgr-|expt_dgr-|math_dgr-", reporter = multi_rep, stop_on_failure = FALSE)
                 '"'"'

azure-pipelines.yml

@@ -71,7 +71,7 @@ jobs:
 - job: build_and_run_tests
   timeoutInMinutes: 360
   pool:
-    vmImage: ubuntu-22.04
+    vmImage: ubuntu-24.04
 
   steps:
     #####################################################################################
@@ -125,11 +125,11 @@ jobs:
     # Install R and all the dependencies dsBaseClient requires.
     # If previous steps have failed then don't run.
   - bash: |
-
-      sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
-      sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/"
-      sudo add-apt-repository ppa:cran/libgit2
-      sudo apt-get update
+      sudo apt-get install --no-install-recommends software-properties-common dirmngr
+      wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+      sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
+      sudo apt-get update -qq
+      sudo apt-get upgrade -y
 
       sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
       sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev -y
@@ -139,7 +139,7 @@ jobs:
       sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
       sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 
-      sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='v6.3.0-dev', dependencies = TRUE)"
+      sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)"
 
       # XML grep for coverage report merging
       sudo apt-get install -qq xml-twig-tools -y
@@ -232,7 +232,7 @@ jobs:
     # Install dsBase.
     # If previous steps have failed then don't run.
   - bash: |
-      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 = 'v6.3.1-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 = '6.3.1'); opal.logout(opal)"
 
       sleep 120
 
@@ -268,7 +268,7 @@ jobs:
       # junit reporter output is to test_results.xml
       #
       # "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
-      # testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
+      # testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
       sudo R -q -e '
         library(covr);
         dsbase.res <- covr::package_coverage(
@@ -283,8 +283,9 @@ jobs:
                 junit_rep <- JunitReporter$new(file = "test_results_dsbase.xml");
                 progress_rep <- ProgressReporter$new(max_failures = 999999);
                 multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
+                options("datashield.return_errors" = FALSE);
                 options("default_driver" = "OpalDriver");
-                testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
+                testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
                 '"'"'
             )
         );
@@ -357,7 +358,7 @@ jobs:
     # If previous steps have failed then don't run
   - bash: |
 
-      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, 'dsDanger', username = 'datashield', ref = 'v6.3.0-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, 'dsDanger', username = 'datashield', ref = '6.3.1'); opal.logout(opal)"
 
     workingDirectory: $(Pipeline.Workspace)/dsBaseClient
     displayName: 'Install dsDanger package on Opal server'
@@ -396,6 +397,7 @@ jobs:
                 junit_rep <- JunitReporter$new(file = "test_results_dsdanger.xml");
                 progress_rep <- ProgressReporter$new(max_failures = 999999);
                 multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
+                options("datashield.return_errors" = FALSE);
                 options("default_driver" = "OpalDriver");
                 testthat::test_package("$(projectName)", filter = "__dgr-|datachk_dgr-|smk_dgr-|arg_dgr-|disc_dgr-|smk_expt_dgr-|expt_dgr-|math_dgr-", reporter = multi_rep, stop_on_failure = FALSE)
                 '"'"'