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(v1.6.0.9040) unit tests
This commit is contained in:
parent
6c3ab19e3a
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33
.github/workflows/check.yaml
vendored
33
.github/workflows/check.yaml
vendored
@ -89,18 +89,10 @@ jobs:
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steps:
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-r@master
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- uses: r-lib/actions/setup-r@v1
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with:
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r-version: ${{ matrix.config.r }}
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# - uses: r-lib/actions/setup-pandoc@master
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# - name: Query dependencies
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# if: matrix.config.r != '3.0'
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# run: |
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# saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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# shell: Rscript {0}
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- name: Install Linux dependencies
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if: runner.os == 'Linux'
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# update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
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@ -108,7 +100,8 @@ jobs:
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run: |
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sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev
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- name: Cache R packages
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- name: Restore cached R packages
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# this step will add the step 'Post Restore cached R packages' on a succesful run
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if: runner.os != 'Windows'
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uses: actions/cache@v1
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with:
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@ -122,7 +115,7 @@ jobs:
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source("data-raw/_install_deps.R")
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shell: Rscript {0}
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- name: Session info
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- name: Show session info
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run: |
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options(width = 100)
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utils::sessionInfo()
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@ -137,8 +130,9 @@ jobs:
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_R_CHECK_DEPENDS_ONLY_: true
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_R_CHECK_LENGTH_1_CONDITION_: verbose
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_R_CHECK_LENGTH_1_LOGIC2_: verbose
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R_LIBS_USER: ${{ env.R_LIBS_USER }}
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R_TINYTEST: true
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# during 'R CMD check', R_LIBS_USER will be overwritten, so:
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R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
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R_RUN_TINYTEST: true
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run: |
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tar -xf data-raw/AMR_latest.tar.gz
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rm -rf AMR/vignettes
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@ -153,8 +147,9 @@ jobs:
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_R_CHECK_DEPENDS_ONLY_: true
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_R_CHECK_LENGTH_1_CONDITION_: verbose
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_R_CHECK_LENGTH_1_LOGIC2_: verbose
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R_LIBS_USER: ${{ env.R_LIBS_USER }}
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R_TINYTEST: true
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# during 'R CMD check', R_LIBS_USER will be overwritten, so:
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R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
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R_RUN_TINYTEST: true
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run: |
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tar -xf data-raw/AMR_latest.tar.gz
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rm -rf AMR/vignettes
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@ -167,9 +162,9 @@ jobs:
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find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
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shell: bash
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- name: Upload check results
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if: failure()
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uses: actions/upload-artifact@master
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- name: Upload artifacts
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if: always()
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uses: actions/upload-artifact@v2
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with:
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name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
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name: artifacts-${{ matrix.config.os }}-r${{ matrix.config.r }}
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path: AMR.Rcheck
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 1.6.0.9038
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Date: 2021-05-15
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Version: 1.6.0.9040
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Date: 2021-05-16
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Title: Antimicrobial Resistance Data Analysis
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Authors@R: c(
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person(role = c("aut", "cre"),
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@ -57,7 +57,7 @@ Suggests:
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skimr,
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tidyr,
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tinytest,
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xml2,
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xml2
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VignetteBuilder: knitr,rmarkdown
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URL: https://msberends.github.io/AMR/, https://github.com/msberends/AMR
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BugReports: https://github.com/msberends/AMR/issues
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4
NEWS.md
4
NEWS.md
@ -1,5 +1,5 @@
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# `AMR` 1.6.0.9035
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## <small>Last updated: 15 May 2021</small>
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# `AMR` 1.6.0.9040
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## <small>Last updated: 16 May 2021</small>
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### New
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* Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()`
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Binary file not shown.
@ -43,5 +43,3 @@ for (i in seq_len(length(to_update))) {
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warning = function(w) message(w$message),
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error = function(e) message(e$message))
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}
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# saveRDS(to_update, ".github/depends.Rds", version = 2)
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9031</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9031</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
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</span>
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</div>
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@ -39,7 +39,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9011</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
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</span>
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</div>
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@ -47,14 +47,14 @@
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<ul class="nav navbar-nav">
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<li>
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<a href="../index.html">
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<span class="fa fa-home"></span>
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<span class="fas fa-home"></span>
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Home
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</a>
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</li>
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<li class="dropdown">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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<span class="fa fa-question-circle"></span>
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<span class="fas fa-question-circle"></span>
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How to
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@ -63,77 +63,77 @@
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="../articles/AMR.html">
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<span class="fa fa-directions"></span>
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<span class="fas fa-directions"></span>
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Conduct AMR analysis
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</a>
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</li>
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<li>
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<a href="../articles/resistance_predict.html">
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<span class="fa fa-dice"></span>
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<span class="fas fa-dice"></span>
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Predict antimicrobial resistance
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</a>
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</li>
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<li>
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<a href="../articles/datasets.html">
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<span class="fa fa-database"></span>
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<span class="fas fa-database"></span>
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Data sets for download / own use
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</a>
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</li>
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<li>
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<a href="../articles/PCA.html">
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<span class="fa fa-compress"></span>
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<span class="fas fa-compress"></span>
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Conduct principal component analysis for AMR
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</a>
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</li>
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<li>
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<a href="../articles/MDR.html">
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<span class="fa fa-skull-crossbones"></span>
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<span class="fas fa-skull-crossbones"></span>
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Determine multi-drug resistance (MDR)
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</a>
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</li>
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<li>
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<a href="../articles/WHONET.html">
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<span class="fa fa-globe-americas"></span>
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<span class="fas fa-globe-americas"></span>
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Work with WHONET data
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</a>
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</li>
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<li>
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<a href="../articles/SPSS.html">
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<span class="fa fa-file-upload"></span>
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<span class="fas fa-file-upload"></span>
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Import data from SPSS/SAS/Stata
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</a>
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</li>
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<li>
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<a href="../articles/EUCAST.html">
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<span class="fa fa-exchange-alt"></span>
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<span class="fas fa-exchange-alt"></span>
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Apply EUCAST rules
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</a>
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</li>
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<li>
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<a href="../reference/mo_property.html">
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<span class="fa fa-bug"></span>
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<span class="fas fa-bug"></span>
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Get properties of a microorganism
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</a>
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</li>
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<li>
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<a href="../reference/ab_property.html">
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<span class="fa fa-capsules"></span>
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<span class="fas fa-capsules"></span>
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Get properties of an antibiotic
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</a>
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</li>
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<li>
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<a href="../articles/benchmarks.html">
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<span class="fa fa-shipping-fast"></span>
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<span class="fas fa-shipping-fast"></span>
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Other: benchmarks
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</a>
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@ -142,21 +142,21 @@
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</li>
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<li>
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<a href="../reference/index.html">
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<span class="fa fa-book-open"></span>
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<span class="fas fa-book-open"></span>
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Manual
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</a>
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</li>
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<li>
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<a href="../authors.html">
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<span class="fa fa-users"></span>
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<span class="fas fa-users"></span>
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Authors
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</a>
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</li>
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<li>
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<a href="../news/index.html">
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<span class="far fa far fa-newspaper"></span>
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<span class="far fa-newspaper"></span>
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Changelog
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</a>
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@ -165,14 +165,14 @@
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<ul class="nav navbar-nav navbar-right">
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<li>
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<a href="https://github.com/msberends/AMR">
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<span class="fab fa fab fa-github"></span>
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<span class="fab fa-github"></span>
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Source Code
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</a>
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</li>
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<li>
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<a href="../survey.html">
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<span class="fa fa-clipboard-list"></span>
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<span class="fas fa-clipboard-list"></span>
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Survey
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</a>
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@ -187,13 +187,12 @@
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</header><link href="datasets_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
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<script src="datasets_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
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</header><script src="datasets_files/header-attrs-2.7/header-attrs.js"></script><div class="row">
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<div class="col-md-9 contents">
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<div class="page-header toc-ignore">
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<h1 data-toc-skip>Data sets for download / own use</h1>
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<h4 class="date">27 April 2021</h4>
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<h4 class="date">16 May 2021</h4>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
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<div class="hidden name"><code>datasets.Rmd</code></div>
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@ -212,7 +211,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
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<a href="#microorganisms-currently-accepted-names" class="anchor"></a>Microorganisms (currently accepted names)</h2>
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<p>A data set with 70,026 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p>
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<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
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<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
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<p>It was last updated on 11 March 2021 20:59:32 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
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<p><strong>Direct download links:</strong></p>
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<ul>
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<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.rds">R file</a> (2.2 MB)<br>
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@ -433,7 +432,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
<p>A data set with 14,100 rows and 4 columns, containing the following column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and <em>prevalence</em>.</p>
|
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<p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e. of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p>
|
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<p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
|
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<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
|
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<p>It was last updated on 5 March 2021 09:46:55 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.rds">R file</a> (0.2 MB)<br>
|
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@ -498,7 +497,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
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<a href="#antibiotic-agents" class="anchor"></a>Antibiotic agents</h2>
|
||||
<p>A data set with 456 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>atc</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
|
||||
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
||||
<p>It was last updated on 4 May 2021 13:38:27 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.rds">R file</a> (32 kB)<br>
|
||||
@ -666,7 +665,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
<a href="#antiviral-agents" class="anchor"></a>Antiviral agents</h2>
|
||||
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
|
||||
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
||||
<p>It was last updated on 29 August 2020 19:53:07 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.rds">R file</a> (5 kB)<br>
|
||||
@ -793,7 +792,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
<a href="#intrinsic-bacterial-resistance" class="anchor"></a>Intrinsic bacterial resistance</h2>
|
||||
<p>A data set with 93,892 rows and 2 columns, containing the following column names:<br><em>microorganism</em> and <em>antibiotic</em>.</p>
|
||||
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
|
||||
<p>It was last updated on 5 March 2021 09:46:55 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.rds">R file</a> (69 kB)<br>
|
||||
@ -1008,7 +1007,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
<a href="#interpretation-from-mic-values-disk-diameters-to-rsi" class="anchor"></a>Interpretation from MIC values / disk diameters to R/SI</h2>
|
||||
<p>A data set with 20,486 rows and 10 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
|
||||
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
|
||||
<p>It was last updated on 5 March 2021 09:46:55 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds">R file</a> (34 kB)<br>
|
||||
@ -1138,7 +1137,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
<a href="#dosage-guidelines-from-eucast" class="anchor"></a>Dosage guidelines from EUCAST</h2>
|
||||
<p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
|
||||
<p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
|
||||
<p>It was last updated on 25 January 2021 20:58:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/dosage.rds">R file</a> (3 kB)<br>
|
||||
|
||||
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9031</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9031</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -42,7 +42,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9031</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9031</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -236,12 +236,12 @@
|
||||
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
|
||||
</div>
|
||||
|
||||
<div id="amr-1609031" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.6.0.9031">
|
||||
<a href="#amr-1609031" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9031</h1>
|
||||
<div id="last-updated-15-may-2021" class="section level2">
|
||||
<div id="amr-1609040" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.6.0.9040">
|
||||
<a href="#amr-1609040" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9040</h1>
|
||||
<div id="last-updated-16-may-2021" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#last-updated-15-may-2021" class="anchor"></a><small>Last updated: 15 May 2021</small>
|
||||
<a href="#last-updated-16-may-2021" class="anchor"></a><small>Last updated: 16 May 2021</small>
|
||||
</h2>
|
||||
<div id="new" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
|
||||
@ -12,7 +12,7 @@ articles:
|
||||
datasets: datasets.html
|
||||
resistance_predict: resistance_predict.html
|
||||
welcome_to_AMR: welcome_to_AMR.html
|
||||
last_built: 2021-05-15T19:35Z
|
||||
last_built: 2021-05-16T07:24Z
|
||||
urls:
|
||||
reference: https://msberends.github.io/AMR//reference
|
||||
article: https://msberends.github.io/AMR//articles
|
||||
|
||||
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9031</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9031</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -134,6 +134,8 @@ echo "•••••••••••••••••"
|
||||
echo "• Building site •"
|
||||
echo "•••••••••••••••••"
|
||||
Rscript -e "suppressMessages(pkgdown::build_site(lazy = $lazy, examples = FALSE))"
|
||||
# always rebuild datasets vignette
|
||||
Rscript -e "pkgdown::build_article('datasets', lazy = FALSE, quiet = TRUE)"
|
||||
# add the survey page
|
||||
Rscript -e "source('data-raw/create_survey_page.R')"
|
||||
echo
|
||||
|
||||
@ -24,12 +24,12 @@
|
||||
# ==================================================================== #
|
||||
|
||||
unjoined <- example_isolates
|
||||
inner <- example_isolates %>% inner_join_microorganisms()
|
||||
left <- example_isolates %>% left_join_microorganisms()
|
||||
semi <- example_isolates %>% semi_join_microorganisms()
|
||||
anti <- example_isolates %>% anti_join_microorganisms()
|
||||
suppressWarnings(right <- example_isolates %>% right_join_microorganisms())
|
||||
suppressWarnings(full <- example_isolates %>% full_join_microorganisms())
|
||||
inner <- inner_join_microorganisms(example_isolates)
|
||||
left <- left_join_microorganisms(example_isolates)
|
||||
semi <- semi_join_microorganisms(example_isolates)
|
||||
anti <- anti_join_microorganisms(example_isolates)
|
||||
suppressWarnings(right <- right_join_microorganisms(example_isolates))
|
||||
suppressWarnings(full <- full_join_microorganisms(example_isolates))
|
||||
|
||||
expect_true(ncol(unjoined) < ncol(inner))
|
||||
expect_true(nrow(unjoined) == nrow(inner))
|
||||
|
||||
@ -24,11 +24,10 @@
|
||||
# ==================================================================== #
|
||||
|
||||
# test only on GitHub Actions and at home - not on CRAN as tests are lengthy
|
||||
if (identical(Sys.getenv("R_TINYTEST"), "true")) {
|
||||
print(Sys.getenv("R_LIBS_USER"))
|
||||
.libPaths(c("/Users/runner/work/_temp/Library", .libPaths()))
|
||||
if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
|
||||
# env var 'R_LIBS_USER' got overwritten during 'R CMD check' in GitHub Actions, so:
|
||||
.libPaths(c(Sys.getenv("R_LIBS_USER_GH_ACTIONS"), .libPaths()))
|
||||
print(.libPaths())
|
||||
print(as.data.frame(utils::installed.packages())[, "Version", drop = FALSE])
|
||||
library(tinytest)
|
||||
library(AMR)
|
||||
test_package("AMR")
|
||||
|
||||
Loading…
Reference in New Issue
Block a user