V6.3.2 test

.Rbuildignore

@@ -17,8 +17,8 @@
 ^R/secure.global.ranking.md$
 ^_pkgdown\.yml$
 ^docs$
-^dsBase_6.3.1.tar.gz$
-^dsBase_6.3.1-permissive.tar.gz$
+^dsBase_6.3.2.tar.gz$
+^dsBase_6.3.2-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 $(lsb_release -cs)-cran40/"
+
               sudo apt-get update -y
               sudo apt-get install -y r-base-core cmake
       - run:
@@ -33,6 +38,9 @@ jobs:
               sudo apt-get install -y libjpeg-dev
       - run:
           command: |
+              sudo Rscript -e "install.packages('devtools', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('covr', dependencies=TRUE)"
+
               sudo Rscript -e "install.packages('fields', dependencies=TRUE)"
               sudo Rscript -e "install.packages('metafor', dependencies=TRUE)"
               sudo Rscript -e "install.packages('meta', dependencies=TRUE)"
@@ -42,6 +50,15 @@ jobs:
               sudo Rscript -e "install.packages('panelaggregation', dependencies=TRUE)"
               sudo Rscript -e "install.packages('methods', dependencies=TRUE)"
               sudo Rscript -e "install.packages('dplyr', dependencies=TRUE)"
+
+              sudo Rscript -e "install.packages('DSI', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('DSOpal', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('DSLite', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('MolgenisAuth', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('MolgenisArmadillo', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('DSMolgenisArmadillo', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('DescTools', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('e1071', dependencies=TRUE)"
       - run:
           command: |
               sudo Rscript -e 'library(covr); covr::codecov(token = "'$CODECOV_TOKEN'", quiet=FALSE)'

DESCRIPTION

@@ -1,8 +1,42 @@
 Package: dsBaseClient
 Title: DataSHIELD Client Functions
-Version: 6.3.1
-Author: DataSHIELD Developers <datashield@liverpool.ac.uk>
-Maintainer: DataSHIELD Developers <datashield@liverpool.ac.uk>
+Version: 6.3.2
+Authors@R: c(person(given = "Paul",
+                    family = "Burton",
+                    role = c("aut")),
+             person(given = "Rebecca",
+                    family = "Wilson",
+                    role = c("aut")),
+             person(given = "Olly",
+                    family = "Butters",
+                    role = c("aut")),
+             person(given = "Patricia",
+                    family = "Ryser-Welch",
+                    role = c("aut")),
+             person(given = "Alex",
+                    family = "Westerberg",
+                    role = c("aut")),
+             person(given = "Leire",
+                    family = "Abarrategui",
+                    role = c("aut")),
+             person(given = "Roberto",
+                    family = "Villegas-Diaz",
+                    role = c("aut"),
+                    comment = c(ORCID = "0000-0001-5036-8661")),
+             person(given = "Demetris",
+                    family = "Avraam",
+                    role = c("aut"),
+                    comment = c(ORCID = "0000-0001-8908-2441")),
+             person(given = "Yannick",
+                    family = "Marcon",
+                    role = c("aut", "cre"),
+                    email = "yannick.marcon@obiba.org",
+                    comment = c(ORCID = "0000-0003-0138-2023")),
+             person(given = "Stuart",
+                    family = "Wheater",
+                    role = c("aut", "cre"),
+                    email = "stuart.wheater@arjuna.com",
+                    comment = c(ORCID = "0009-0003-2419-1964")))
 Description: DataSHIELD client functions for the client side.
 License: GPL-3
 Depends:
@@ -19,6 +53,14 @@ 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

@@ -17,7 +17,7 @@
 #' 
 #' Many GLMs can be fitted very simply using a formula such as:
 #' 
-#' \deqn{y~a+b+c+d} 
+#' \eqn{y~a+b+c+d}
 #' 
 #' which simply means fit a GLM with \code{y} as the outcome variable and 
 #' \code{a}, \code{b}, \code{c} and \code{d} as covariates. 
@@ -26,7 +26,7 @@
 #' Instead, if you need to fit a more complex
 #' model, for example:
 #' 
-#'  \deqn{EVENT~1+TID+SEXF*AGE.60}
+#'  \eqn{EVENT~1+TID+SEXF*AGE.60}
 #'
 #' In the above model the outcome variable is \code{EVENT} 
 #' and the  covariates 

R/ds.glmSLMA.R

@@ -61,7 +61,7 @@
 #' 
 #' Many glms can be fitted very simply using a formula such as:
 #' 
-#' \deqn{y~a+b+c+d} 
+#' \eqn{y~a+b+c+d}
 #' 
 #' which simply means fit a glm with \code{y} as the outcome variable and 
 #' \code{a}, \code{b}, \code{c} and \code{d} as covariates. 
@@ -70,7 +70,7 @@
 #' Instead, if you need to fit a more complex
 #' model, for example:
 #' 
-#'  \deqn{EVENT~1+TID+SEXF*AGE.60}
+#' \eqn{EVENT~1+TID+SEXF*AGE.60}
 #'
 #' In the above model the outcome variable is \code{EVENT} 
 #' and the  covariates 

R/ds.glmerSLMA.R

@@ -18,17 +18,17 @@
 #' In \code{formula} most shortcut notation allowed by \code{glmer()} function is
 #' also allowed by \code{ds.glmerSLMA}. 
 #' Many GLMEs can be fitted very simply using a formula like:
-#' \deqn{y~a+b+(1|c)} 
+#' \eqn{y~a+b+(1|c)}
 #' which simply means fit an GLME  with \code{y} as the outcome variable (e.g. 
 #' a binary case-control using a logistic regression model or a count or a survival
 #' time using a Poisson regression model), \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)} 
+#' \eqn{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 formulas such as: \eqn{y~a+b+(1|c/d)}
-#' or \eqn{y~a+b+(1|c)+(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

R/ds.lmerSLMA.R

@@ -18,12 +18,12 @@
 #' 
 #' 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)}
+#' \eqn{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)}
+#' \eqn{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)}.

R/ds.rBinom.R

@@ -216,10 +216,11 @@ single.integer.seed<-c(single.integer.seed,seed.as.integer.study.specific)
 if(seed.as.text=="NULL"){
 cat("NO SEED SET IN STUDY",study.id,"\n\n")
 
-}
+} else {
   calltext <- paste0("setSeedDS(", seed.as.text, ")")
   ssDS.obj[[study.id]] <- DSI::datashield.aggregate(datasources[study.id], as.symbol(calltext))
 }
+}
 cat("\n\n")
 
 

R/ds.rUnif.R

@@ -234,9 +234,10 @@ single.integer.seed<-c(single.integer.seed,seed.as.integer.study.specific)
 if(seed.as.text=="NULL"){
 cat("NO SEED SET IN STUDY",study.id,"\n")
 
-}
+} else {
   calltext <- paste0("setSeedDS(", seed.as.text, ")")
   ssDS.obj[[study.id]] <- DSI::datashield.aggregate(datasources[study.id], as.symbol(calltext))
+}
 } 
 
 

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 - v6.3.2-dev
     branches:
       include:
-      - v6.3.1-dev
+      - v6.3.2-dev
     always: true
 
 #########################################################################################
@@ -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
@@ -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_6.3.1-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_6.3.2-permissive.tar.gz" -X POST http://localhost:8080/install-package
       sleep 60
 
       docker container restart dsbaseclient_armadillo_1
@@ -263,7 +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
 
@@ -364,7 +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_6.3.2.tar.gz" -X POST http://localhost:8080/install-package
 
       docker container restart dsbaseclient_armadillo_1
       sleep 60
@@ -387,7 +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 - v6.3.2-dev
     branches:
       include:
-      - v6.3.1-dev
+      - v6.3.2-dev
     always: true
 
 #########################################################################################
@@ -133,13 +133,14 @@ jobs:
 
       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
+      sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
       sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
       sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table','panelaggregation'), dependencies=TRUE, repos='https://cloud.r-project.org')"
       sudo R -q -e "install.packages(c('DSI','DSOpal','DSLite'), dependencies=TRUE, repos='https://cloud.r-project.org')"
       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='6.3.2', dependencies = TRUE)"
 
       # XML grep for coverage report merging
       sudo apt-get install -qq xml-twig-tools -y
@@ -185,7 +186,7 @@ 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
@@ -232,9 +233,11 @@ 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(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)"
 
-      sleep 120
+      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 = '6.3.2'); opal.logout(opal)"
+
+      sleep 60
 
       R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); opal.logout(opal)"
 
@@ -258,7 +261,7 @@ 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
 
@@ -358,6 +361,8 @@ jobs:
     # If previous steps have failed then don't run
   - 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, 'dsDanger', username = 'datashield', ref = '6.3.1'); opal.logout(opal)"
 
     workingDirectory: $(Pipeline.Workspace)/dsBaseClient
@@ -374,9 +379,8 @@ 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
 
       # run the coverage tool and output to coveragelist.csv

docker-compose_armadillo.yml

@@ -3,7 +3,7 @@ services:
         hostname: armadillo
         ports:
             - 8080:8080
-        image: datashield/armadillo_citest:4.11.1
+        image: datashield/armadillo_citest:5.0.0.2
         environment:
             LOGGING_CONFIG: 'classpath:logback-file.xml'
             AUDIT_LOG_PATH: '/app/logs/audit.log'
@@ -16,6 +16,6 @@ services:
 
     default:
         hostname: default
-        image: datashield/rock-knot-devel-permissive:latest
+        image: datashield/rserver-neutron:latest
         environment:
             DEBUG: "FALSE"

docker-compose_opal.yml

@@ -1,6 +1,6 @@
 services:
     opal:
-        image: obiba/opal:5.0.1
+        image: obiba/opal:5.1.4
         ports:
             - "8443:8443"
         links:
@@ -20,4 +20,4 @@ services:
             - MONGO_INITDB_ROOT_USERNAME=root
             - MONGO_INITDB_ROOT_PASSWORD=foobar
     rock:
-        image: datashield/rock-knot-devel-permissive:latest
+        image: datashield/rock-margin-joule-permissive:latest