datashield · StuartWheater · Oct 14, 2024 · Oct 14, 2024 · Oct 15, 2024 · Oct 15, 2024
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -20,3 +20,5 @@
 ^dsBase_6.3.1.tar.gz$
 ^dsBase_6.3.1-permissive.tar.gz$
 ^dsDanger_6.3.1.tar.gz$
+^\.circleci$
+^\.circleci/config\.yml$
diff --git a/.circleci/config.yml b/.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
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -6,8 +6,8 @@ Maintainer: DataSHIELD Developers <[email protected]>
 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,

diff --git a/R/ds.glm.R b/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

diff --git a/R/ds.glmSLMA.R b/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

diff --git a/R/ds.glmerSLMA.R b/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

diff --git a/R/ds.lmerSLMA.R b/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)
 #'   

diff --git a/README.md b/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

diff --git a/armadillo_azure-pipelines.yml b/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 +125,10 @@ jobs:
     # Install R and all the dependencies dsBaseClient requires.
     # If previous steps have failed then don't run.
   - bash: |
-
-      sudo apt-get update -qq
       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
@@ -289,6 +288,7 @@ 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-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
                 '"'"'
@@ -410,6 +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)
                 '"'"'

diff --git a/azure-pipelines.yml b/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:
     #####################################################################################
@@ -125,16 +125,11 @@ jobs:
     # Install R and all the dependencies dsBaseClient requires.
     # If previous steps have failed then don't run.
   - bash: |
-
-      sudo apt update -qq
-      sudo apt install --no-install-recommends software-properties-common dirmngr
+      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-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 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
@@ -288,6 +283,7 @@ 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-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
                 '"'"'
@@ -401,6 +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)
                 '"'"'

diff --git a/docker-compose_armadillo.yml b/docker-compose_armadillo.yml
@@ -3,7 +3,7 @@ services:
         hostname: armadillo
         ports:
             - 8080:8080
-        image: datashield/armadillo_citest:4.10.0
+        image: datashield/armadillo_citest:4.11.1
         environment:
             LOGGING_CONFIG: 'classpath:logback-file.xml'
             AUDIT_LOG_PATH: '/app/logs/audit.log'

diff --git a/docker-compose_opal.yml b/docker-compose_opal.yml
@@ -1,6 +1,6 @@
 services:
     opal:
-        image: obiba/opal:5.0.0-RC5
+        image: obiba/opal:5.0.1
         ports:
             - "8443:8443"
         links: