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(v1.7.1.9039) reinitiate all units tests

development
parent
commit
5f433d6e5c
  1. 12
      .github/workflows/check.yaml
  2. 4
      DESCRIPTION
  3. 4
      NEWS.md
  4. BIN
      data-raw/AMR_latest.tar.gz
  5. 6
      docs/articles/datasets.html
  6. 12
      docs/news/index.html
  7. 1
      inst/tinytest/test-ab_class_selectors.R
  8. 2
      tests/tinytest.R

12
.github/workflows/check.yaml

@ -128,18 +128,6 @@ jobs: @@ -128,18 +128,6 @@ jobs:
as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
shell: Rscript {0}
# - name: Only keep vignettes on release version
- name: Remove vignettes
# if: matrix.config.r != 'release'
if: always()
# writing to DESCRIPTION2 and then moving to DESCRIPTION is required for R < 3.3 as writeLines() cannot overwrite
run: |
rm -rf AMR/vignettes
Rscript -e "writeLines(readLines('AMR/DESCRIPTION')[!grepl('VignetteBuilder', readLines('AMR/DESCRIPTION'))], 'AMR/DESCRIPTION2')"
rm AMR/DESCRIPTION
mv AMR/DESCRIPTION2 AMR/DESCRIPTION
shell: bash
- name: Run R CMD check
if: always()
env:

4
DESCRIPTION

@ -1,6 +1,6 @@ @@ -1,6 +1,6 @@
Package: AMR
Version: 1.7.1.9038
Date: 2021-09-01
Version: 1.7.1.9039
Date: 2021-09-03
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by

4
NEWS.md

@ -1,5 +1,5 @@ @@ -1,5 +1,5 @@
# `AMR` 1.7.1.9038
## <small>Last updated: 1 September 2021</small>
# `AMR` 1.7.1.9039
## <small>Last updated: 3 September 2021</small>
### Breaking changes
* Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version

BIN
data-raw/AMR_latest.tar.gz

Binary file not shown.

6
docs/articles/datasets.html

@ -44,7 +44,7 @@ @@ -44,7 +44,7 @@
</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">1.7.1.9038</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9039</span>
</span>
</div>
@ -190,7 +190,7 @@ @@ -190,7 +190,7 @@
<div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">01 September 2021</h4>
<h4 data-toc-skip class="date">03 September 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="hidden name"><code>datasets.Rmd</code></div>
@ -495,7 +495,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi @@ -495,7 +495,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<a href="#antibiotic-agents" class="anchor" aria-hidden="true"></a>Antibiotic agents</h2>
<p>A data set with 456 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</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 19 August 2021 21:21:57 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 2 September 2021 11:50:06 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" class="external-link">R file</a> (32 kB)<br>

12
docs/news/index.html

@ -92,7 +92,7 @@ @@ -92,7 +92,7 @@
</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">1.7.1.9038</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9039</span>
</span>
</div>
@ -240,12 +240,12 @@ @@ -240,12 +240,12 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1719038" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9038">
<a href="#amr-1719038" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9038</h1>
<div id="last-updated-1-september-2021" class="section level2">
<div id="amr-1719039" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9039">
<a href="#amr-1719039" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9039</h1>
<div id="last-updated-3-september-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-1-september-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 1 September 2021</small>
<a href="#last-updated-3-september-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 3 September 2021</small>
</h2>
<div id="breaking-changes" class="section level3">
<h3 class="hasAnchor">

1
inst/tinytest/test-ab_class_selectors.R

@ -56,6 +56,7 @@ expect_equal(ncol(example_isolates[, c("mo", aminoglycosides())]), 5, tolerance @@ -56,6 +56,7 @@ expect_equal(ncol(example_isolates[, c("mo", aminoglycosides())]), 5, tolerance
expect_equal(ncol(example_isolates[, c(administrable_per_os() & penicillins())]), 5, tolerance = 0.5)
expect_equal(ncol(example_isolates[, c(administrable_iv() & penicillins())]), 7, tolerance = 0.5)
expect_equal(ncol(example_isolates[, c(administrable_iv() | penicillins())]), 37, tolerance = 0.5)
# filter using any() or all()
expect_equal(nrow(example_isolates[any(carbapenems() == "R"), ]), 55, tolerance = 0.5)

2
tests/tinytest.R

@ -34,13 +34,11 @@ if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) { @@ -34,13 +34,11 @@ if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
"inst/tinytest",
"tinytest"),
verbose = 99,
pattern = "first.*\\.[rR]$",
color = FALSE)
cat("SUMMARY:\n")
print(summary(out))
cat("WARNINGS:\n")
print(warnings())
cat(attributes(out)$duration, "\n")
}
}

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