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AMR
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(v1.7.1.9043) unit tests

This commit is contained in:
dr. M.S. (Matthijs) Berends 2021-09-29 20:10:44 +02:00
parent 0775802b7f
commit 45f597cac5
8 changed files with 31 additions and 25 deletions
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30
.github/workflows/check.yaml vendored
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@ -84,13 +84,7 @@ jobs:
R_REPOSITORIES: "https://cran.rstudio.com"
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
R_KEEP_PKG_SOURCE: yes
R_CHECK_CRAN_INCOMING: false
R_CHECK_FORCE_SUGGESTS: false
R_CHECK_DEPENDS_ONLY: true
R_CHECK_LENGTH_1_CONDITION: verbose
R_CHECK_LENGTH_1_LOGIC2: verbose
R_RUN_TINYTEST: true
steps:
- uses: actions/checkout@v2
@ -101,11 +95,18 @@ jobs:
r-version: ${{ matrix.config.r }}
http-user-agent: ${{ matrix.config.http-user-agent }}
use-public-rspm: true
- uses: r-lib/actions/setup-r-dependencies@v1
with:
extra-packages: rcmdcheck
- name: show file list
run: ls -lh
shell: bash
- name: Install dependencies
if: always()
run: |
install.packages("remotes")
remotes::install_local("data-raw/AMR_latest.tar.gz", dependencies = TRUE)
shell: Rscript {0}
- name: Show session info
if: always()
run: |
@ -116,10 +117,15 @@ jobs:
- uses: r-lib/actions/check-r-package@v1
env:
_R_CHECK_CRAN_INCOMING_: false
_R_CHECK_FORCE_SUGGESTS_: false
_R_CHECK_DEPENDS_ONLY_: true
_R_CHECK_LENGTH_1_CONDITION_: verbose
_R_CHECK_LENGTH_1_LOGIC2_: verbose
R_RUN_TINYTEST: true
# during 'R CMD check', R_LIBS_USER will be overwritten, so:
R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
- name: Show unit tests output
if: always()
run: find check -name 'tinytest.Rout*' -exec cat '{}' \; || true

6
.github/workflows/codecovr.yaml vendored
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@ -26,11 +26,11 @@
on:
push:
branches:
- premaster
- master
- development
- main
pull_request:
branches:
- master
- main
name: code-coverage

6
.github/workflows/lintr.yaml vendored
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@ -26,11 +26,11 @@
on:
push:
branches:
- premaster
- master
- development
- main
pull_request:
branches:
- master
- main
name: lintr

2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.7.1.9041
Version: 1.7.1.9043
Date: 2021-09-29
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

2
NEWS.md
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@ -1,4 +1,4 @@
# `AMR` 1.7.1.9041
# `AMR` 1.7.1.9043
## <small>Last updated: 29 September 2021</small>
### Breaking changes

BIN
data-raw/AMR_latest.tar.gz
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2
docs/articles/datasets.html
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@ -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">1.7.1.9041</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9043</span>
</span>
</div>

8
docs/news/index.html
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@ -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">1.7.1.9041</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9043</span>
</span>
</div>
@ -240,9 +240,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1719041" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9041">
<a href="#amr-1719041" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9041</h1>
<div id="amr-1719043" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9043">
<a href="#amr-1719043" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9043</h1>
<div id="last-updated-29-september-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-29-september-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 29 September 2021</small>