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AMR
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(v1.6.0.9026) new unit test flow

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dr. M.S. (Matthijs) Berends 2021-05-13 21:16:22 +02:00
parent 994d157aa6
commit b1d942be91
14 changed files with 26 additions and 20 deletions
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11
.github/workflows/check.yaml vendored
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@ -102,12 +102,13 @@ jobs:
shell: Rscript {0}
- name: Query dependencies
if: matrix.config.r != '3.0'
run: |
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
shell: Rscript {0}
- name: Cache R packages
if: runner.os != 'Windows'
if: runner.os != 'Windows' && matrix.config.r != '3.0'
# && matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
uses: actions/cache@v1
with:
@ -145,7 +146,8 @@ jobs:
_R_CHECK_LENGTH_1_LOGIC2_: verbose
run: |
tar -xf data-raw/AMR_latest.tar.gz
R CMD check AMR -no-manual -as-cran
rm -rf AMR/vignettes
R CMD check AMR
shell: bash
- name: Run R CMD check on Linux and macOS
@ -158,12 +160,15 @@ jobs:
_R_CHECK_LENGTH_1_LOGIC2_: verbose
run: |
tar -xf data-raw/AMR_latest.tar.gz
rm -rf AMR/vignettes
R CMD check AMR --no-manual --as-cran
shell: bash
- name: Show testthat output
if: always()
run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
run: |
ls -lh
find check -name 'testthat.Rout*' -exec cat '{}' \; || true
shell: bash
- name: Upload check results

2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.6.0.9025
Version: 1.6.0.9026
Date: 2021-05-13
Title: Antimicrobial Resistance Data Analysis
Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# `AMR` 1.6.0.9025
# `AMR` 1.6.0.9026
## <small>Last updated: 13 May 2021</small>
### New

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data-raw/AMR_latest.tar.gz
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2
docs/404.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9026</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -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">1.6.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9026</span>
</span>
</div>

2
docs/articles/index.html
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@ -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">1.6.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9026</span>
</span>
</div>

2
docs/authors.html
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@ -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">1.6.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9026</span>
</span>
</div>

2
docs/index.html
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@ -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">1.6.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9026</span>
</span>
</div>

14
docs/news/index.html
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@ -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">1.6.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9026</span>
</span>
</div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1609023" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9023">
<a href="#amr-1609023" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9023</h1>
<div id="amr-1609026" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9026">
<a href="#amr-1609026" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9026</h1>
<div id="last-updated-13-may-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-13-may-2021" class="anchor"></a><small>Last updated: 13 May 2021</small>
@ -262,7 +262,7 @@
<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>
</ul>
</li>
<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>
<li>Added <code>ggplot()</code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
</li>
</ul>
</div>
@ -348,7 +348,7 @@
<span class="co">#&gt; Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
</li>
<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>
<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
<li><p><code>ggplot()</code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
<li>
<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>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
@ -405,7 +405,7 @@
<li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
<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>
<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>
<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>
<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>
</ul>
</li>
<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>

2
docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-05-13T17:31Z
last_built: 2021-05-13T19:15Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

2
docs/reference/index.html
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@ -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">1.6.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9026</span>
</span>
</div>

2
docs/survey.html
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@ -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">1.6.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9026</span>
</span>
</div>

1
tests/testthat/test-atc_online.R
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@ -27,6 +27,7 @@ context("atc_online.R")
test_that("atc_online works", {
skip_on_cran()
skip_if_not_installed("curl")
skip_if_not(curl::has_internet())
expect_gte(length(atc_online_groups(ab_atc("AMX"))), 1)