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StuartWheaterStuartWheater
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Merge pull request datashield#635 from StuartWheater/v7.0-dev
Align version with 7.0/7.0.0
2 parents 020b172 + ca06f10 commit ac77774

7 files changed

Lines changed: 46 additions & 47 deletions

‎.Rbuildignore‎

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@@ -17,8 +17,8 @@
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^R/secure.global.ranking.md$
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^_pkgdown\.yml$
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^docs$
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^dsBase_7.0-dev-feat_performance\.tar\.gz$
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^dsBase_7.0-dev-feat_performance-permissive\.tar\.gz$
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^dsBase_7.0.0\.tar\.gz$
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^dsBase_7.0.0-permissive\.tar\.gz$
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^dsDanger_6.3.4.tar.gz$
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^\.circleci$
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^\.circleci/config\.yml$

‎.github/workflows/dsBaseClient_test_suite.yaml‎

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@@ -23,7 +23,7 @@ jobs:
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timeout-minutes: 120
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permissions:
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contents: read
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# These should all be constant, except TEST_FILTER. This can be used to test
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# subsets of test files in the testthat directory. Options are like:
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# '*' <- Run all tests.
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_r_check_system_clock_: 0
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WORKFLOW_ID: ${{ github.run_id }}-${{ github.run_attempt }}
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PROJECT_NAME: dsBaseClient
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BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
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BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
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REPO_OWNER: ${{ github.repository_owner }}
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R_KEEP_PKG_SOURCE: yes
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GITHUB_TOKEN: ${{ github.token || 'placeholder-token' }}
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path: testStatus
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persist-credentials: false
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token: ${{ env.GITHUB_TOKEN }}
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- name: Uninstall default MySQL
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run: |
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curl https://bazel.build/bazel-release.pub.gpg | sudo apt-key add -
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sudo apt-get autoremove -y
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sudo apt-get autoclean -y
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sudo rm -rf /var/lib/mysql/
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev xml-twig-tools -y
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sudo R -q -e "install.packages(c('devtools','covr','fields','meta','metafor','ggplot2','gridExtra','data.table','DSI','DSOpal','DSLite','MolgenisAuth','MolgenisArmadillo','DSMolgenisArmadillo','DescTools','e1071'), repos='https://cloud.r-project.org')"
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sudo R -q -e "devtools::install_github(repo='datashield/dsDangerClient', ref=Sys.getenv('BRANCH_NAME'))"
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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dependencies: 'c("Imports")'
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extra-packages: |
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any::rcmdcheck
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cran::devtools
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cran::git2r
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cran::RCurl
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cran::readr
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cran::magrittr
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cran::xml2
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cran::purrr
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cran::dplyr
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cran::stringr
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cran::tidyr
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cran::quarto
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cran::knitr
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cran::kableExtra
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cran::rmarkdown
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cran::downlit
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extra-packages: |
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any::rcmdcheck
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cran::devtools
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cran::git2r
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cran::RCurl
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cran::readr
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cran::magrittr
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cran::xml2
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cran::purrr
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cran::dplyr
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cran::stringr
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cran::tidyr
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cran::quarto
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cran::knitr
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cran::kableExtra
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cran::rmarkdown
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cran::downlit
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needs: check
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- name: Check manual updated
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run: |
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orig_sum=$(find man -type f | sort -u | xargs cat | md5sum)
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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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working-directory: dsBaseClient
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continue-on-error: true
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- name: Start Armadillo docker-compose
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run: docker compose -f docker-compose_armadillo.yml up -d --build
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working-directory: dsBaseClient
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- name: Install dsBase to Armadillo
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run: |
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curl -u admin:admin -X GET http://localhost:8080/packages
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curl -u admin:admin -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.4-permissive.tar.gz" -X POST http://localhost:8080/install-package
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curl -u admin:admin -H 'Content-Type: multipart/form-data' -F "file=@dsBase_7.0.0-permissive.tar.gz" -X POST http://localhost:8080/install-package
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sleep 60
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docker restart dsbaseclient-armadillo-1
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sleep 30
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curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase
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working-directory: dsBaseClient
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- name: Run tests with coverage & JUnit report
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run: |
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mkdir -p logs
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),
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"coveragelist.csv"
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)'
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mv coveragelist.csv logs/
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mv test_* logs/
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working-directory: dsBaseClient
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- name: Check for JUnit errors
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run: |
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issue_count=$(sed 's/failures="0" errors="0"//' test_results.xml | grep -c errors= || true)
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echo "os:$(lsb_release -ds)" >> ${{ env.WORKFLOW_ID }}.txt
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echo "R:$(R --version | head -n1)" >> ${{ env.WORKFLOW_ID }}.txt
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working-directory: dsBaseClient/logs
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- name: Parse results from testthat and covr
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run: |
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Rscript --verbose --vanilla ../testStatus/source/parse_test_report.R logs/
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working-directory: dsBaseClient
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- name: Render report
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run: |
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cd testStatus
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mkdir -p new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
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mkdir -p new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
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mkdir -p new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest/
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# Copy logs to new logs directory location
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cp -rv ../dsBaseClient/logs/* new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
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cp -rv ../dsBaseClient/logs/${{ env.WORKFLOW_ID }}.txt new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
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R -e 'input_dir <- file.path("../new/logs", Sys.getenv("PROJECT_NAME"), Sys.getenv("BRANCH_NAME"), Sys.getenv("WORKFLOW_ID")); quarto::quarto_render("source/test_report.qmd", execute_params = list(input_dir = input_dir))'
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mv source/test_report.html new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/index.html
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cp -r new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/* new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest
214-
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env:
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PROJECT_NAME: ${{ env.PROJECT_NAME }}
217217
BRANCH_NAME: ${{ env.BRANCH_NAME }}
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WORKFLOW_ID: ${{ env.WORKFLOW_ID }}
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219+
220220
- name: Upload test logs
221221
uses: actions/upload-artifact@v4
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with:
@@ -242,4 +242,3 @@ jobs:
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R -e 'sessionInfo()'
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sudo apt install tree -y
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tree .
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‎armadillo_azure-pipelines.yml‎

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- master
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always: true
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- cron: "0 2 * * *"
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displayName: Nightly build - v7.0-dev-feat/performance
61+
displayName: Nightly build - v7.0-dev
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branches:
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include:
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- v7.0-dev-feat/performance
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- v7.0-dev
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always: true
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6767
#########################################################################################
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curl -u admin:admin -X GET http://localhost:8080/packages
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238-
curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_7.0-dev-feat_performance-permissive.tar.gz" -X POST http://localhost:8080/install-package
238+
curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_7.0.0-permissive.tar.gz" -X POST http://localhost:8080/install-package
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sleep 60
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docker container restart dsbaseclient_armadillo_1

‎azure-pipelines.yml‎

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- master
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always: true
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- cron: "0 2 * * *"
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displayName: Nightly build - v7.0-dev-feat/performance
47+
displayName: Nightly build - v7.0-dev
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branches:
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include:
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- v7.0-dev-feat/performance
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- v7.0-dev
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always: true
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5353
#########################################################################################
@@ -216,7 +216,7 @@ jobs:
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- bash: |
217217
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)"
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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 = '7.0-dev-feat_performance'); opal.logout(opal)"
219+
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 = 'v7.0-dev'); opal.logout(opal)"
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sleep 60
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dsBase_7.0-dev-feat_performance.tar.gz renamed to dsBase_7.0.0-permissive.tar.gz

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dsBase_7.0-dev-feat_performance-permissive.tar.gz renamed to dsBase_7.0.0.tar.gz

3.18 MB
Binary file not shown.

‎opal_azure-pipelines.yml‎

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@@ -58,10 +58,10 @@ schedules:
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- master
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always: true
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- cron: "0 2 * * *"
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displayName: Nightly build - v7.0-dev-feat/performance
61+
displayName: Nightly build - v7.0-dev
6262
branches:
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include:
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- v7.0-dev-feat/performance
64+
- v7.0-dev
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always: true
6666

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#########################################################################################
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- bash: |
236236
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)"
237237
238-
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 = '7.0-dev-feat/performance'); opal.logout(opal)"
238+
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 = 'v7.0-dev'); opal.logout(opal)"
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240240
sleep 60
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