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(v1.6.0.9026) new unit test flow
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parent
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commit
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11
.github/workflows/check.yaml
vendored
11
.github/workflows/check.yaml
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@ -102,12 +102,13 @@ jobs:
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shell: Rscript {0}
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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: Cache R packages
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if: runner.os != 'Windows'
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if: runner.os != 'Windows' && matrix.config.r != '3.0'
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# && matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
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uses: actions/cache@v1
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with:
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@ -145,7 +146,8 @@ jobs:
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_R_CHECK_LENGTH_1_LOGIC2_: verbose
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run: |
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tar -xf data-raw/AMR_latest.tar.gz
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R CMD check AMR -no-manual -as-cran
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rm -rf AMR/vignettes
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R CMD check AMR
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shell: bash
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- name: Run R CMD check on Linux and macOS
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@ -158,12 +160,15 @@ jobs:
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_R_CHECK_LENGTH_1_LOGIC2_: verbose
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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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R CMD check AMR --no-manual --as-cran
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shell: bash
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- name: Show testthat output
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if: always()
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run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
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run: |
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ls -lh
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find check -name 'testthat.Rout*' -exec cat '{}' \; || true
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shell: bash
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- name: Upload check results
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@ -1,5 +1,5 @@
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Package: AMR
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Version: 1.6.0.9025
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Version: 1.6.0.9026
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Date: 2021-05-13
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Title: Antimicrobial Resistance Data Analysis
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
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# `AMR` 1.6.0.9025
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# `AMR` 1.6.0.9026
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## <small>Last updated: 13 May 2021</small>
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### New
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Binary file not shown.
@ -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">1.6.0.9023</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9026</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">1.6.0.9023</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9026</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">1.6.0.9023</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9026</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">1.6.0.9023</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9026</span>
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</span>
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</div>
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@ -42,7 +42,7 @@
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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">1.6.0.9023</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9026</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">1.6.0.9023</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9026</span>
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</span>
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</div>
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@ -236,9 +236,9 @@
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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<div id="amr-1609023" class="section level1">
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<h1 class="page-header" data-toc-text="1.6.0.9023">
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<a href="#amr-1609023" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9023</h1>
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<div id="amr-1609026" class="section level1">
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<h1 class="page-header" data-toc-text="1.6.0.9026">
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<a href="#amr-1609026" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9026</h1>
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<div id="last-updated-13-may-2021" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-13-may-2021" class="anchor"></a><small>Last updated: 13 May 2021</small>
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@ -262,7 +262,7 @@
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<li>The documentation of the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/key_antimicrobials.html">key_antimicrobials()</a></code> functions has been completely rewritten.</li>
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</ul>
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</li>
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<li>Added <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
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<li>Added <code>ggplot()</code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
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</li>
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</ul>
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</div>
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@ -348,7 +348,7 @@
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<span class="co">#> Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
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</li>
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<li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
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<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code><mic></code> and <code><disk></code></p></li>
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<li><p><code>ggplot()</code> generics for classes <code><mic></code> and <code><disk></code></p></li>
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<li>
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<p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
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<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
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@ -405,7 +405,7 @@
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<li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
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<li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
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<li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
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<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> on any vector of MIC and disk diffusion values</li>
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<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
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</ul>
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</li>
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<li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>
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@ -12,7 +12,7 @@ articles:
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datasets: datasets.html
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resistance_predict: resistance_predict.html
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welcome_to_AMR: welcome_to_AMR.html
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last_built: 2021-05-13T17:31Z
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last_built: 2021-05-13T19:15Z
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urls:
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reference: https://msberends.github.io/AMR//reference
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article: https://msberends.github.io/AMR//articles
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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">1.6.0.9023</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9026</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">1.6.0.9023</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9026</span>
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</span>
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</div>
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@ -27,6 +27,7 @@ context("atc_online.R")
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test_that("atc_online works", {
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skip_on_cran()
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skip_if_not_installed("curl")
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skip_if_not(curl::has_internet())
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expect_gte(length(atc_online_groups(ab_atc("AMX"))), 1)
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