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Merge pull request datashield#550 from StuartWheater/v6.4.0-dev
V6.4.0 dev
2 parents 59fd13b + 755a030 commit 465e65b

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‎.Rbuildignore‎

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^docs$
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^dsBase_6.3.1.tar.gz$
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^dsBase_6.3.1-permissive.tar.gz$
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^dsDanger_6.3.0.tar.gz$
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^dsDanger_6.3.1.tar.gz$

‎.circleci/config.yml‎

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# Copyright (c) 2024 Arjuna Technologies, Newcastle upon Tyne. All rights reserved.
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version: 2.1
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jobs:
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dsbaseclient:
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docker:
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- image: cimg/base:current
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resource_class: small
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steps:
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- checkout
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- setup_remote_docker:
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docker_layout_caching: true
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- run: |
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echo "Building"
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echo " Repo Name: " $CIRCLE_PROJECT_REPONAME
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echo " Branch: " $CIRCLE_BRANCH
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echo " Tag: " $CIRCLE_TAG
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- run:
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command: |
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sudo apt-get update -y
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sudo apt-get install -y r-base-core cmake
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- run:
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command: |
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sudo apt-get install -y libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev
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sudo apt-get install -y libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev
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- run:
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command: |
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sudo Rscript -e "install.packages('devtools', dependencies=TRUE)"
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sudo Rscript -e "install.packages('covr', dependencies=TRUE)"
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sudo Rscript -e "install.packages('fields', dependencies=TRUE)"
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sudo Rscript -e "install.packages('meta', dependencies=TRUE)"
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sudo Rscript -e "install.packages('metafor', dependencies=TRUE)"
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sudo Rscript -e "install.packages('ggplot2', dependencies=TRUE)"
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sudo Rscript -e "install.packages('gridExtra', dependencies=TRUE)"
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sudo Rscript -e "install.packages('data.table', dependencies=TRUE)"
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sudo Rscript -e "install.packages('panelaggregation', dependencies=TRUE)"
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sudo Rscript -e "install.packages('DSI', dependencies=TRUE)"
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sudo Rscript -e "install.packages('DSOpal', dependencies=TRUE)"
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sudo Rscript -e "install.packages('DSLite', dependencies=TRUE)"
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sudo Rscript -e "install.packages('MolgenisAuth', dependencies=TRUE)"
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sudo Rscript -e "install.packages('MolgenisArmadillo', dependencies=TRUE)"
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sudo Rscript -e "install.packages('DSMolgenisArmadillo', dependencies=TRUE)"
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sudo Rscript -e "install.packages('DescTools', dependencies=TRUE)"
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sudo Rscript -e "install.packages('e1071', dependencies=TRUE)"
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sudo Rscript -e "install.packages('RANN', dependencies=TRUE)"
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sudo Rscript -e "install.packages('stringr', dependencies=TRUE)"
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sudo Rscript -e "install.packages('lme4', dependencies=TRUE)"
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sudo Rscript -e "install.packages('dplyr', dependencies=TRUE)"
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sudo Rscript -e "install.packages('reshape2', dependencies=TRUE)"
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sudo Rscript -e "install.packages('polycor', dependencies=TRUE)"
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sudo Rscript -e "install.packages('splines', dependencies=TRUE)"
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sudo Rscript -e "install.packages('gamlss', dependencies=TRUE)"
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sudo Rscript -e "install.packages('gamlss.dist', dependencies=TRUE)"
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sudo Rscript -e "install.packages('mice', dependencies=TRUE)"
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sudo Rscript -e "install.packages('childsds', dependencies=TRUE)"
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sudo Rscript -e "install.packages('xml2', dependencies=TRUE)"
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sudo Rscript -e "install.packages('covr', dependencies=TRUE)"
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- run:
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command: |
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sudo Rscript -e 'library(covr); options("default_driver"="DSLiteDriver"); covr::codecov(token="'$CODECOV_TOKEN'", quiet=FALSE)'
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workflows:
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build:
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jobs:
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- dsbaseclient

‎DESCRIPTION‎

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Package: dsBaseClient
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Title: DataSHIELD Client Functions
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Version: 6.3.1.9000
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Version: 6.3.1
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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.
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dplyr
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Suggests:
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testthat
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RoxygenNote: 7.3.1
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RoxygenNote: 7.3.2
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Encoding: UTF-8

‎armadillo_azure-pipelines.yml‎

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# If previous steps have failed then don't run.
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- bash: |
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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 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 $(lsb_release -cs)-cran40/"
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sudo apt-get upgrade -y
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sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
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sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev -y
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sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
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sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"
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sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='v6.3.0-dev', dependencies = TRUE)"
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sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)"
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# XML grep for coverage report merging
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sudo apt-get install -qq xml-twig-tools -y
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# junit reporter output is to test_results.xml
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#
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# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
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# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
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# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
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sudo R -q -e '
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library(covr);
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dsbase.res <- covr::package_coverage(
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progress_rep <- ProgressReporter$new(max_failures = 999999);
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multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
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options("default_driver" = "ArmadilloDriver");
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testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
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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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)
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);

‎azure-pipelines.yml‎

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# If previous steps have failed then don't run.
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- bash: |
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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 update -qq
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sudo apt 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 install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
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sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
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sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"
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sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='v6.3.0-dev', dependencies = TRUE)"
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sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)"
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# XML grep for coverage report merging
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sudo apt-get install -qq xml-twig-tools -y
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# Install dsBase.
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# If previous steps have failed then don't run.
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- bash: |
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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 = 'v6.3.1-dev'); opal.logout(opal)"
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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)"
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sleep 120
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# junit reporter output is to test_results.xml
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#
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# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
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# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
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# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
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sudo R -q -e '
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library(covr);
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dsbase.res <- covr::package_coverage(
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progress_rep <- ProgressReporter$new(max_failures = 999999);
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multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
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options("default_driver" = "OpalDriver");
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testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
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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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)
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);
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# If previous steps have failed then don't run
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- bash: |
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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 = 'v6.3.0-dev'); opal.logout(opal)"
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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)"
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workingDirectory: $(Pipeline.Workspace)/dsBaseClient
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displayName: 'Install dsDanger package on Opal server'

‎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:4.8.1
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image: datashield/armadillo_citest:4.10.0
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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'
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default:
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hostname: default
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image: datashield/rock-junction-devel-permissive:latest
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image: datashield/rock-knot-devel-permissive:latest
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environment:
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DEBUG: "FALSE"

‎docker-compose_opal.yml‎

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services:
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opal:
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image: obiba/opal:4.7.2
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image: obiba/opal:5.0.0-RC5
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ports:
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- "8443:8443"
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links:
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- MONGO_INITDB_ROOT_USERNAME=root
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- MONGO_INITDB_ROOT_PASSWORD=foobar
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rock:
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image: datashield/rock-junction-devel-permissive:latest
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image: datashield/rock-knot-devel-permissive:latest

‎docs/404.html‎

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‎docs/LICENSE.html‎

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