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Merge pull request #363 from datashield/v6.3.1-RC5-dev
Last RC5 Updates
2 parents 5e01ab6 + 517ba9d commit 6690502

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‎.Rbuildignore‎

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^data$
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^docs$
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^pkgdown$
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^\.circleci$
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^\.circleci/config\.yml$

‎.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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dsbase:
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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
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- run:
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command: |
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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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sudo Rscript -e "install.packages('devtools', dependencies=TRUE)"
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sudo Rscript -e "install.packages('DSI', dependencies=TRUE)"
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sudo Rscript -e "install.packages('DSLite', dependencies=TRUE)"
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- run:
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command: |
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sudo Rscript -e 'library(covr); covr::codecov(token = "'$CODECOV_TOKEN'")'
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workflows:
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build:
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jobs:
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- dsbase

‎DESCRIPTION‎

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Package: dsBase
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Title: DataSHIELD server site base functions
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Description: DataSHIELD server site base functions.
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Version: 6.3.1.9000
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Title: DataSHIELD Server Site Base Functions
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Description: DataSHIELD Server Site Base Functions.
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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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License: GPL-3
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Depends:
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R (>= 3.5.0)
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R (>= 4.0.0)
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Imports:
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RANN,
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stringr,

‎R/cDS.R‎

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# check if the output is valid and output accordingly
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if(length(x) < nfilter.tab){
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if(length(x == 0)){
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if(length(x) == 0){
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x <- c()
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}else{
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x <- rep(NA, length(x))

‎README.md‎

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DataSHIELD server side base R library.
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| Branch | dsBase status | dsBaseClient status | dsBaseClient tests |
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| -------- | ------------ | ------------------- | ------------------ |
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| 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/) |
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| 6.2.0 | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBase?branchName=6.2.0)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=3&branchName=6.2.0) | [Tests](https://datashield.github.io/testStatus/dsBase/6.2.0/latest/) | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBaseClient?branchName=6.2.0)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=6.2.0) | [Tests](https://datashield.github.io/testStatus/dsBaseClient/6.2.0/latest/) |
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| 6.3.0 | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBase?branchName=6.3.0)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=3&branchName=6.3.0) | [Tests](https://datashield.github.io/testStatus/dsBase/6.3.0/latest/) | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBaseClient?branchName=6.3.0)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=6.3.0) | [Tests](https://datashield.github.io/testStatus/dsBaseClient/6.3.0/latest/) |
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| 6.3.1-dev | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBase?branchName=v6.3.1-dev)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=3&branchName=v6.3.1-dev) | [Tests](https://datashield.github.io/testStatus/dsBase/v6.3.1-dev/latest/) | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBaseClient?branchName=v6.3.1-dev)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=v6.3.1-dev) | [Tests](https://datashield.github.io/testStatus/dsBaseClient/v6.3.1-dev/latest/) |
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[![License](https://img.shields.io/badge/license-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.html)
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About
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=====
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DataSHIELD is a software package which allows you to do non-disclosive federated analysis on sensitive data. Our website (https://www.datashield.org) has in depth descriptions of what it is, how it works and how to install it. A key point to highlight is that DataSHIELD has a client-server infrastructure, so the dsBase package (https://github.com/datashield/dsBase) needs to be used in conjuction with the dsBaseClient package (https://github.com/datashield/dsBaseClient) - trying to use one without the other makes no sense.
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Detailed instructions on how to install DataSHIELD are at https://www.datashield.org/wiki. The code here is organised as:
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Detailed instructions on how to install DataSHIELD are at https://wiki.datashield.org/. The code here is organised as:
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| Location | What is it? |

‎azure-pipelines.yml‎

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branches:
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include:
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- master
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- 6.2.0
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- 6.3.0
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always: true
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- cron: "0 1 * * *"
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jobs:
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- job: run_devtools_check
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timeoutInMinutes: 90
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timeoutInMinutes: 120
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pool:
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vmImage: ubuntu-latest
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vmImage: ubuntu-24.04
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steps:
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# Install R and all the dependencies dsBase 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 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 -qq
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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 pkg-config -y
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sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgit2-dev libharfbuzz-dev libfribidi-dev -y
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sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgit2-dev libharfbuzz-dev libfribidi-dev libfontconfig1-dev -y
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sudo apt-get install -qq libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev -y
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sudo apt-get install -qq r-base -y
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sudo R -e "install.packages('devtools', dependencies=TRUE)"
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sudo R -e "install.packages('RANN', dependencies=TRUE)"
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# If this step fails still mark as failed, but don't stop the rest of the steps running.
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- bash: |
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R -q -e "library('devtools'); devtools::check(args = c('--no-examples'))" | tee azure-pipelines_check.Rout
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R -q -e "library('devtools'); devtools::check(args = c('--no-tests', '--no-examples'))" | tee azure-pipelines_check.Rout
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grep --quiet "^0 errors" azure-pipelines_check.Rout && grep --quiet " 0 warnings" azure-pipelines_check.Rout && grep --quiet " 0 notes" azure-pipelines_check.Rout
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- bash: |
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# Any of the below makes the tests work.
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sudo R --verbose -e 'devtools::check()'
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sudo R --verbose -e 'devtools::reload()'
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pwd
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mkdir $(Pipeline.Workspace)/logs

‎docs/404.html‎

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