Merge branch 'v6.4.0-dev' into v6.4.0-dev

Author: StuartWheater

.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$

.circleci/config.yml

@@ -5,7 +5,8 @@ version: 2.1
 jobs:
   dsbaseclient:
     docker:
-      - image: cimg/base:current
+#      - image: cimg/base:current
+      - image: cimg/base:2024.11
     resource_class: small
     steps:
       - checkout
@@ -18,6 +19,10 @@ jobs:
           echo "  Tag:       " $CIRCLE_TAG
       - run:
           command: |
+              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 -y "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
+
               sudo apt-get update -y
               sudo apt-get install -y r-base-core cmake
       - run:
@@ -31,20 +36,20 @@ jobs:
               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('devtools', dependencies=TRUE)"
               sudo Rscript -e "install.packages('covr', dependencies=TRUE)"
 
               sudo Rscript -e "install.packages('fields', dependencies=TRUE)"
-              sudo Rscript -e "install.packages('meta', 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)"
               sudo Rscript -e "install.packages('DSI', dependencies=TRUE)"
               sudo Rscript -e "install.packages('DSOpal', dependencies=TRUE)"
               sudo Rscript -e "install.packages('DSLite', dependencies=TRUE)"

DESCRIPTION

@@ -6,8 +6,8 @@ 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,
@@ -19,6 +19,14 @@ Imports:
     methods,
     dplyr
 Suggests:
-    testthat
+    lme4,
+    httr,
+    tibble,
+    testthat,
+    e1071,
+    DescTools,
+    DSOpal,
+    DSMolgenisArmadillo,
+    DSLite
 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: \code{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: \code{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: 
-#' \code{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

@@ -58,10 +58,10 @@ schedules:
       - master
     always: true
   - cron: "0 2 * * *"
-    displayName: Nightly build - v6.3.1-dev
+    displayName: Nightly build - v6.4.0-dev
     branches:
       include:
-      - v6.3.1-dev
+      - v6.4.0-dev
     always: true
 
 #########################################################################################
@@ -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
@@ -186,7 +185,7 @@ jobs:
     # If this step fails still mark as failed, but don't stop the rest of the steps running.    
   - bash: |
 
-      R -q -e "library('devtools'); devtools::check(args = c('--no-examples'))" | tee azure-pipelines_check.Rout
+      R -q -e "library('devtools'); devtools::check(args = c('--no-examples', '--no-tests'))" | tee azure-pipelines_check.Rout
       grep --quiet "^0 errors" azure-pipelines_check.Rout && grep --quiet " 0 warnings" azure-pipelines_check.Rout && grep --quiet " 0 notes" azure-pipelines_check.Rout
 
     workingDirectory: $(Pipeline.Workspace)/dsBaseClient
@@ -236,7 +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_6.3.1-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_6.4.0.9000-permissive.tar.gz" -X POST http://localhost:8080/install-package
       sleep 60
 
       docker container restart dsbaseclient_armadillo_1
@@ -264,7 +263,7 @@ jobs:
       # best guess is that there is an implicit build or similar that happens. Although
       # I cannot replicate that directly with build etc directly.
 
-      sudo R --verbose -e 'devtools::check()'
+      sudo R --verbose -e 'devtools::reload()'
 
       mkdir $(Pipeline.Workspace)/logs
 
@@ -365,7 +364,7 @@ jobs:
   - bash: |
       curl -u admin:admin http://localhost:8080/whitelist
 
-      curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.1.tar.gz" -X POST http://localhost:8080/install-package
+      curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.4.0.9000.tar.gz" -X POST http://localhost:8080/install-package
 
       docker container restart dsbaseclient_armadillo_1
       sleep 60
@@ -388,7 +387,7 @@ jobs:
   - bash: |
 
       # See, 'Code coverage and JUnit report output' for issues with the approach and improvement needed.
-      sudo R --verbose -e 'devtools::check()'
+      sudo R --verbose -e 'devtools::reload()'
 
       pwd
       mkdir $(Pipeline.Workspace)/logs

azure-pipelines.yml

@@ -58,10 +58,10 @@ schedules:
       - master
     always: true
   - cron: "0 2 * * *"
-    displayName: Nightly build - v6.3.1-dev
+    displayName: Nightly build - v6.4.0-dev
     branches:
       include:
-      - v6.3.1-dev
+      - v6.4.0-dev
     always: true
 
 #########################################################################################
@@ -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='6.3.1', dependencies = TRUE)"
+      sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.4.0', dependencies = TRUE)"
 
       # XML grep for coverage report merging
       sudo apt-get install -qq xml-twig-tools -y
@@ -185,7 +185,7 @@ jobs:
     # If this step fails still mark as failed, but don't stop the rest of the steps running.    
   - bash: |
 
-      R -q -e "library('devtools'); devtools::check(args = c('--no-examples'))" | tee azure-pipelines_check.Rout
+      R -q -e "library('devtools'); devtools::check(args = c('--no-examples', '--no-tests'))" | tee azure-pipelines_check.Rout
       grep --quiet "^0 errors" azure-pipelines_check.Rout && grep --quiet " 0 warnings" azure-pipelines_check.Rout && grep --quiet " 0 notes" azure-pipelines_check.Rout
 
     workingDirectory: $(Pipeline.Workspace)/dsBaseClient
@@ -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 = '6.3.1'); 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 = '6.4.0'); opal.logout(opal)"
 
       sleep 120
 
@@ -258,7 +258,7 @@ jobs:
       # best guess is that there is an implicit build or similar that happens. Although
       # I cannot replicate that directly with build etc directly.
 
-      sudo R --verbose -e 'devtools::check()'
+      sudo R --verbose -e 'devtools::reload()'
 
       mkdir $(Pipeline.Workspace)/logs
 
@@ -374,7 +374,7 @@ jobs:
   - bash: |
 
       # See, 'Code coverage and JUnit report output' for issues with the approach and improvement needed.
-      sudo R --verbose -e 'devtools::check()'
+      sudo R --verbose -e 'devtools::reload()'
 
       pwd
       mkdir $(Pipeline.Workspace)/logs