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StuartWheaterStuartWheater
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Merge pull request datashield#565 from StuartWheater/v6.4.0-dev
Merge changes for V6.4.0 dev
2 parents 7abd6e6 + 63eaae4 commit e3c8f0f

7 files changed

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‎DESCRIPTION‎

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Package: dsBaseClient
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Title: DataSHIELD Client Functions
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Version: 6.3.1
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Version: 6.4.0.9000
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Author: DataSHIELD Developers <datashield@liverpool.ac.uk>
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Maintainer: DataSHIELD Developers <datashield@liverpool.ac.uk>
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Description: DataSHIELD client functions for the client side.

‎armadillo_azure-pipelines.yml‎

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junit_rep <- JunitReporter$new(file = "test_results_dsbase.xml");
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progress_rep <- ProgressReporter$new(max_failures = 999999);
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multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
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options("datashield.return_errors" = FALSE);
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options("default_driver" = "ArmadilloDriver");
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testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
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'"'"'
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junit_rep <- JunitReporter$new(file = "test_results_dsdanger.xml");
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progress_rep <- ProgressReporter$new(max_failures = 999999);
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multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
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options("datashield.return_errors" = FALSE);
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options("default_driver" = "ArmadilloDriver");
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testthat::test_package("$(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)
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'"'"'

‎azure-pipelines.yml‎

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- job: build_and_run_tests
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timeoutInMinutes: 360
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pool:
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vmImage: ubuntu-22.04
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vmImage: ubuntu-24.04
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steps:
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#####################################################################################
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# Install R and all the dependencies dsBaseClient requires.
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# If previous steps have failed then don't run.
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- bash: |
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sudo apt update -qq
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sudo apt install --no-install-recommends software-properties-common dirmngr
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sudo apt-get install --no-install-recommends software-properties-common dirmngr
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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
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sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
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# sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
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# sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/"
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# sudo add-apt-repository ppa:cran/libgit2
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sudo apt-get update
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sudo apt-get update -qq
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sudo apt-get upgrade -y
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sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
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sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev -y
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junit_rep <- JunitReporter$new(file = "test_results_dsbase.xml");
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progress_rep <- ProgressReporter$new(max_failures = 999999);
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multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
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options("datashield.return_errors" = FALSE);
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options("default_driver" = "OpalDriver");
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testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
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'"'"'
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junit_rep <- JunitReporter$new(file = "test_results_dsdanger.xml");
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progress_rep <- ProgressReporter$new(max_failures = 999999);
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multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
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options("datashield.return_errors" = FALSE);
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options("default_driver" = "OpalDriver");
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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)
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'"'"'

‎docker-compose_armadillo.yml‎

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hostname: armadillo
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ports:
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- 8080:8080
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image: datashield/armadillo_citest:4.10.0
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image: datashield/armadillo_citest:4.11.1
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environment:
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LOGGING_CONFIG: 'classpath:logback-file.xml'
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AUDIT_LOG_PATH: '/app/logs/audit.log'

‎docker-compose_opal.yml‎

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services:
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opal:
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image: obiba/opal:5.0.0-RC5
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image: obiba/opal:5.0.0
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ports:
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- "8443:8443"
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links:

‎opal_azure-pipelines.yml‎

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- job: build_and_run_tests
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timeoutInMinutes: 360
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pool:
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vmImage: ubuntu-22.04
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vmImage: ubuntu-24.04
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steps:
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#####################################################################################
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# Install R and all the dependencies dsBaseClient requires.
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# If previous steps have failed then don't run.
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- bash: |
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sudo apt-get update
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sudo apt-get install --no-install-recommends software-properties-common dirmngr
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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
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sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
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sudo apt-get update -qq
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sudo apt-get upgrade -y
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sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
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junit_rep <- JunitReporter$new(file = "test_results_dsbase.xml");
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progress_rep <- ProgressReporter$new(max_failures = 999999);
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multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
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options("datashield.return_errors" = FALSE);
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options("default_driver" = "OpalDriver");
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testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
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'"'"'
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junit_rep <- JunitReporter$new(file = "test_results_dsdanger.xml");
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progress_rep <- ProgressReporter$new(max_failures = 999999);
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multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
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options("datashield.return_errors" = FALSE);
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options("default_driver" = "OpalDriver");
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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)
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'"'"'

‎tests/testthat/perf_files/default_perf_profile.csv‎

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"refer_name","rate","lower_tolerance","upper_tolerance"
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"conndisconn::perf::simple0","0.1050","0.5","2"
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"ds.abs::perf::0","3.896","0.5","2"
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"ds.asInteger::perf:0","3.550","0.5","2"
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"ds.asList::perf:0","8.040","0.5","2"
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"ds.asNumeric::perf:0","3.577","0.5","2"
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"ds.assign::perf::0","6.739","0.5","2"
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"ds.class::perf::combine:0","8.171","0.5","2"
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"ds.colnames::perf:0","6.292","0.5","2"
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"ds.exists::perf::combine:0","16.33","0.5","2"
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"ds.length::perf::combine:0","16.08","0.5","2"
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"ds.mean::perf::combine:0","16.08","0.5","2"
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"ds.mean::perf::split:0","15.83","0.5","2"
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"void::perf::void::0","36510.0","0.5","2"
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"conndisconn::perf::simple0","0.229","0.5","2"
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"ds.abs::perf::0","1.796","0.5","2"
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"ds.asInteger::perf:0","1.538","0.5","2"
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"ds.asList::perf:0","3.061","0.5","2"
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"ds.asNumeric::perf:0","1.548","0.5","2"
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"ds.assign::perf::0","3.556","0.5","2"
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"ds.class::perf::combine:0","3.149","0.5","2"
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"ds.colnames::perf:0","2.584","0.5","2"
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"ds.exists::perf::combine:0","7.138","0.5","2"
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"ds.length::perf::combine:0","6.385","0.5","2"
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"ds.mean::perf::combine:0","5.982","0.5","2"
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"ds.mean::perf::split:0","6.923","0.5","2"
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"void::perf::void::0","41810.0","0.5","2"

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