V6.3.2 dev

.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:

armadillo_azure-pipelines.yml

@@ -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

azure-pipelines.yml

@@ -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

docker-compose_armadillo.yml

@@ -16,6 +16,6 @@ services:
 
     default:
         hostname: default
-        image: datashield/rock-knot-devel-permissive:latest
+        image: datashield/rock-lemon-donkey-permissive:latest
         environment:
             DEBUG: "FALSE"

docker-compose_opal.yml

@@ -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-lemon-donkey-permissive:latest

opal_azure-pipelines.yml

@@ -186,7 +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

tests/docker/armadillo/standard/config/application.yml

@@ -14,11 +14,17 @@ armadillo:
   # oidc-admin-user: user@yourdomain.org
   profiles:
     - name: default
-      image: datashield/rock-knot-devel-permissive:latest
+      image: datashield/rock-lemon-donkey-permissive:latest
       port: 8085
       host: default
-      package-whitelist:
+      package-whitelist: # Packages for 'donkey'
         - dsBase
+        - dsMediation
+        - dsMTLBase
+        - dsSurvival
+        - dsTidyverse
+        - dsExposome
+        - dsOmics
         - resourcer
       function-blacklist: [ ]
       options:

tests/testthat.R

@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(dsBaseClient)
+
+test_check("dsBaseClient")

tests/testthat/perf_files/armadillo_azure-pipeline.csv

@@ -1,14 +1,14 @@
 "refer_name","rate","lower_tolerance","upper_tolerance"
-"conndisconn::perf::simple0","0.1050","0.5","2"
-"ds.abs::perf::0","3.896","0.5","2"
-"ds.asInteger::perf:0","3.550","0.5","2"
-"ds.asList::perf:0","8.040","0.5","2"
-"ds.asNumeric::perf:0","3.577","0.5","2"
-"ds.assign::perf::0","6.739","0.5","2"
-"ds.class::perf::combine:0","8.171","0.5","2"
-"ds.colnames::perf:0","6.292","0.5","2"
-"ds.exists::perf::combine:0","16.33","0.5","2"
-"ds.length::perf::combine:0","16.08","0.5","2"
-"ds.mean::perf::combine:0","16.08","0.5","2"
-"ds.mean::perf::split:0","15.83","0.5","2"
-"void::perf::void::0","36510.0","0.5","2"
+"conndisconn::perf::simple0","0.1275","0.5","2"
+"ds.abs::perf::0","4.824","0.5","2"
+"ds.asInteger::perf:0","4.366","0.5","2"
+"ds.asList::perf:0","9.787","0.5","2"
+"ds.asNumeric::perf:0","4.316","0.5","2"
+"ds.assign::perf::0","8.055","0.5","2"
+"ds.class::perf::combine:0","9.847","0.5","2"
+"ds.colnames::perf:0","7.574","0.5","2"
+"ds.exists::perf::combine:0","19.84","0.5","2"
+"ds.length::perf::combine:0","19.58","0.5","2"
+"ds.mean::perf::combine:0","19.66","0.5","2"
+"ds.mean::perf::split:0","19.21","0.5","2"
+"void::perf::void::0","41810.0","0.5","2"

tests/testthat/perf_files/default_perf_profile.csv

@@ -1,14 +1,14 @@
 "refer_name","rate","lower_tolerance","upper_tolerance"
-"conndisconn::perf::simple0","0.229","0.5","2"
-"ds.abs::perf::0","1.796","0.5","2"
-"ds.asInteger::perf:0","1.538","0.5","2"
-"ds.asList::perf:0","3.061","0.5","2"
-"ds.asNumeric::perf:0","1.548","0.5","2"
-"ds.assign::perf::0","3.556","0.5","2"
-"ds.class::perf::combine:0","3.149","0.5","2"
-"ds.colnames::perf:0","2.584","0.5","2"
-"ds.exists::perf::combine:0","7.138","0.5","2"
-"ds.length::perf::combine:0","6.385","0.5","2"
-"ds.mean::perf::combine:0","5.982","0.5","2"
-"ds.mean::perf::split:0","6.923","0.5","2"
-"void::perf::void::0","41810.0","0.5","2"
+"conndisconn::perf::simple0","0.2118","0.5","2"
+"ds.abs::perf::0","1.718","0.5","2"
+"ds.asInteger::perf:0","1.484","0.5","2"
+"ds.asList::perf:0","3.050","0.5","2"
+"ds.asNumeric::perf:0","1.508","0.5","2"
+"ds.assign::perf::0","3.547","0.5","2"
+"ds.class::perf::combine:0","3.061","0.5","2"
+"ds.colnames::perf:0","2.456","0.5","2"
+"ds.exists::perf::combine:0","6.904","0.5","2"
+"ds.length::perf::combine:0","6.058","0.5","2"
+"ds.mean::perf::combine:0","5.892","0.5","2"
+"ds.mean::perf::split:0","6.881","0.5","2"
+"void::perf::void::0","27070.0","0.5","2"

tests/testthat/perf_files/dslite_hp-laptop_quay.csv

@@ -0,0 +1,14 @@
+"refer_name","rate","lower_tolerance","upper_tolerance"
+"conndisconn::perf::simple0","1.28701068653782","0.5","2"
+"ds.abs::perf::0","9.58736733800142","0.5","2"
+"ds.asInteger::perf:0","8.50891366904172","0.5","2"
+"ds.asList::perf:0","16.5820946915488","0.5","2"
+"ds.asNumeric::perf:0","9.11018116242571","0.5","2"
+"ds.assign::perf::0","20.7627800741047","0.5","2"
+"ds.class::perf::combine:0","16.4968034024194","0.5","2"
+"ds.colnames::perf:0","12.2919611789594","0.5","2"
+"ds.exists::perf::combine:0","41.3622556042039","0.5","2"
+"ds.length::perf::combine:0","41.0818690662793","0.5","2"
+"ds.mean::perf::combine:0","40.9888639028757","0.5","2"
+"ds.mean::perf::split:0","41.2851424288384","0.5","2"
+"void::perf::void::0","24346.5613457168","0.5","2"

tests/testthat/perf_files/opal_azure-pipeline.csv

@@ -1,14 +1,14 @@
 "refer_name","rate","lower_tolerance","upper_tolerance"
-"conndisconn::perf::simple0","0.229","0.5","2"
-"ds.abs::perf::0","1.796","0.5","2"
-"ds.asInteger::perf:0","1.538","0.5","2"
-"ds.asList::perf:0","3.061","0.5","2"
-"ds.asNumeric::perf:0","1.548","0.5","2"
-"ds.assign::perf::0","3.556","0.5","2"
-"ds.class::perf::combine:0","3.149","0.5","2"
-"ds.colnames::perf:0","2.584","0.5","2"
-"ds.exists::perf::combine:0","7.138","0.5","2"
-"ds.length::perf::combine:0","6.385","0.5","2"
-"ds.mean::perf::combine:0","5.982","0.5","2"
-"ds.mean::perf::split:0","6.923","0.5","2"
-"void::perf::void::0","41810.0","0.5","2"
+"conndisconn::perf::simple0","0.2118","0.5","2"
+"ds.abs::perf::0","1.718","0.5","2"
+"ds.asInteger::perf:0","1.484","0.5","2"
+"ds.asList::perf:0","3.050","0.5","2"
+"ds.asNumeric::perf:0","1.508","0.5","2"
+"ds.assign::perf::0","3.547","0.5","2"
+"ds.class::perf::combine:0","3.061","0.5","2"
+"ds.colnames::perf:0","2.456","0.5","2"
+"ds.exists::perf::combine:0","6.904","0.5","2"
+"ds.length::perf::combine:0","6.058","0.5","2"
+"ds.mean::perf::combine:0","5.892","0.5","2"
+"ds.mean::perf::split:0","6.881","0.5","2"
+"void::perf::void::0","27070.0","0.5","2"

tests/testthat/perf_files/opal_hp-laptop_quay.csv

@@ -1,14 +1,14 @@
 "refer_name","rate","lower_tolerance","upper_tolerance"
-"conndisconn::perf::simple0","0.145258829974366","0.5","2"
-"ds.abs::perf::0","0.685354162883962","0.5","2"
-"ds.asInteger::perf:0","0.757343916339244","0.5","2"
-"ds.asList::perf:0","1.39411478465579","0.5","2"
-"ds.asNumeric::perf:0","0.695929483688074","0.5","2"
-"ds.assign::perf::0","1.98579096107968","0.5","2"
-"ds.class::perf::combine:0","1.83959664387857","0.5","2"
-"ds.colnames::perf:0","1.38390626627527","0.5","2"
-"ds.exists::perf::combine:0","4.37111331491725","0.5","2"
-"ds.length::perf::combine:0","2.99769707214692","0.5","2"
-"ds.mean::perf::combine:0","3.14458208946095","0.5","2"
-"ds.mean::perf::split:0","4.258064355457","0.5","2"
-"void::perf::void::0","20588.7831697084","0.5","2"
+"conndisconn::perf::simple0","0.163258942292474","0.5","2"
+"ds.abs::perf::0","0.855013692368105","0.5","2"
+"ds.asInteger::perf:0","0.788986058823576","0.5","2"
+"ds.asList::perf:0","1.77505549252221","0.5","2"
+"ds.asNumeric::perf:0","0.877591207737289","0.5","2"
+"ds.assign::perf::0","2.08707546713196","0.5","2"
+"ds.class::perf::combine:0","1.65635603819885","0.5","2"
+"ds.colnames::perf:0","1.33221754701434","0.5","2"
+"ds.exists::perf::combine:0","4.18346517297051","0.5","2"
+"ds.length::perf::combine:0","3.45700158311582","0.5","2"
+"ds.mean::perf::combine:0","3.36796688580702","0.5","2"
+"ds.mean::perf::split:0","4.11472547478384","0.5","2"
+"void::perf::void::0","23198.7075219865","0.5","2"

tests/testthat/perf_files/template_perf_profile.csv

@@ -0,0 +1 @@
+"refer_name","rate","lower_tolerance","upper_tolerance"