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AMR
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(v1.6.0.9030) new unit test flow

This commit is contained in:
dr. M.S. (Matthijs) Berends 2021-05-13 23:07:31 +02:00
parent c17acbe712
commit 9a381c8d18
16 changed files with 28 additions and 21 deletions
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4
.github/workflows/check.yaml vendored
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@ -144,6 +144,7 @@ jobs:
_R_CHECK_DEPENDS_ONLY_: true
_R_CHECK_LENGTH_1_CONDITION_: verbose
_R_CHECK_LENGTH_1_LOGIC2_: verbose
R_LIBS_USER: ${{ env.R_LIBS_USER }}
run: |
tar -xf data-raw/AMR_latest.tar.gz
rm -rf AMR/vignettes
@ -158,10 +159,11 @@ jobs:
_R_CHECK_DEPENDS_ONLY_: true
_R_CHECK_LENGTH_1_CONDITION_: verbose
_R_CHECK_LENGTH_1_LOGIC2_: verbose
R_LIBS_USER: ${{ env.R_LIBS_USER }}
run: |
tar -xf data-raw/AMR_latest.tar.gz
rm -rf AMR/vignettes
R CMD check AMR --no-manual --as-cran --no-vignettes --library='/Users/runner/work/_temp/Library'
R CMD check AMR --no-manual --no-vignettes
shell: bash
- name: Show testthat output

2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.6.0.9028
Version: 1.6.0.9030
Date: 2021-05-13
Title: Antimicrobial Resistance Data Analysis
Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# `AMR` 1.6.0.9028
# `AMR` 1.6.0.9030
## <small>Last updated: 13 May 2021</small>
### New

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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">1.6.0.9028</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9030</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">1.6.0.9028</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9030</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">1.6.0.9028</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9030</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">1.6.0.9028</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9030</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">1.6.0.9028</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9030</span>
</span>
</div>

8
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">1.6.0.9028</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9030</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-1609028" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9028">
<a href="#amr-1609028" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9028</h1>
<div id="amr-1609030" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9030">
<a href="#amr-1609030" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9030</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>

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: 2021-05-13T20:43Z
last_built: 2021-05-13T21:04Z
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">1.6.0.9028</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9030</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">1.6.0.9028</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9030</span>
</span>
</div>

5
tests/testthat.R
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@ -27,7 +27,10 @@
# able to install it. Yet, we want basic R CMD CHECK's in those R versions
# as well, so only run unit tests in later R versions:
if (require("testthat", warn.conflicts = FALSE)) {
library(testthat)
library(AMR)
# print non-base packages
print(as.data.frame(utils::installed.packages())[which(is.na(as.data.frame(utils::installed.packages())$Priority)),
"Version",
drop = FALSE])
test_check("AMR")
}

2
tests/testthat/test-mdro.R
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@ -119,7 +119,7 @@ test_that("mdro works", {
pza = sample_rsi(),
MFX = sample_rsi(),
KAN = sample_rsi())
expect_gt(n_distinct(mdr_tb(x)), 2)
expect_gt(length(unique(mdr_tb(x))), 2)
# check the guideline by Magiorakos et al. (2012), the default guideline
stau <- data.frame(mo = c("S. aureus", "S. aureus", "S. aureus", "S. aureus"),

10
tests/testthat/test-resistance_predict.R
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@ -48,10 +48,12 @@ test_that("prediction of rsi works", {
info = TRUE)))
pdf(NULL) # prevent Rplots.pdf being created
expect_silent(plot(x))
expect_silent(ggplot_rsi_predict(x))
expect_silent(ggplot(x))
expect_error(ggplot_rsi_predict(example_isolates))
if (suppressWarnings(require("ggplot2"))) {
expect_silent(ggplot_rsi_predict(x))
expect_silent(ggplot(x))
expect_error(ggplot_rsi_predict(example_isolates))
}
expect_output(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "AMX",