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AMR
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(v1.7.1.9046) unit tests

This commit is contained in:
dr. M.S. (Matthijs) Berends 2021-10-03 13:50:52 +02:00
parent b0c84cce9c
commit 9b97233be2
7 changed files with 63 additions and 42 deletions
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79
.github/workflows/check.yaml vendored
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@ -77,36 +77,40 @@ jobs:
- {os: windows-latest, r: '3.4', allowfail: false}
- {os: windows-latest, r: '3.3', allowfail: false}
- {os: windows-latest, r: '3.2', allowfail: false}
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
RSPM: ${{ matrix.config.rspm }}
R_REPOSITORIES: "https://cran.rstudio.com"
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
R_KEEP_PKG_SOURCE: yes
steps:
- uses: actions/checkout@v2
- uses: r-lib/actions/setup-pandoc@v1
- uses: r-lib/actions/setup-r@v1
with:
r-version: ${{ matrix.config.r }}
http-user-agent: ${{ matrix.config.http-user-agent }}
use-public-rspm: true
- name: show file list
run: ls -lh
shell: bash
- name: Install dependencies
- name: Install Linux dependencies
if: runner.os == 'Linux'
# update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
# we don't want to depend on the sysreqs pkg here, as it requires quite a recent R version
# as of May 2021: https://sysreqs.r-hub.io/pkg/AMR,R,cleaner,curl,dplyr,ggplot2,ggtext,knitr,microbenchmark,pillar,readxl,rmarkdown,rstudioapi,rvest,skimr,tidyr,tinytest,xml2,backports,crayon,rlang,vctrs,evaluate,highr,markdown,stringr,yaml,xfun,cli,ellipsis,fansi,lifecycle,utf8,glue,mime,magrittr,stringi,generics,R6,tibble,tidyselect,pkgconfig,purrr,digest,gtable,isoband,MASS,mgcv,scales,withr,nlme,Matrix,farver,labeling,munsell,RColorBrewer,viridisLite,lattice,colorspace,gridtext,Rcpp,RCurl,png,jpeg,bitops,cellranger,progress,rematch,hms,prettyunits,htmltools,jsonlite,tinytex,base64enc,httr,selectr,openssl,askpass,sys,repr,cpp11
run: |
sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev
- name: Restore cached R packages
# this step will add the step 'Post Restore cached R packages' on a succesful run
if: runner.os != 'Windows'
uses: actions/cache@v1
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-v4
- name: Unpack AMR and install R dependencies
if: always()
run: |
install.packages("remotes", repos = c("https://cloud.r-project.org", "https://cran.rstudio.com"))
remotes::install_local("data-raw/AMR_latest.tar.gz", dependencies = TRUE)
shell: Rscript {0}
tar -xf data-raw/AMR_latest.tar.gz
Rscript -e "source('data-raw/_install_deps.R')"
shell: bash
- name: Show session info
if: always()
run: |
@ -114,26 +118,43 @@ jobs:
utils::sessionInfo()
as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
shell: Rscript {0}
- uses: r-lib/actions/check-r-package@v1
# # - 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:
_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
R_RUN_TINYTEST: true
run: |
R CMD check --no-manual --run-donttest --run-dontrun AMR
shell: bash
- name: Upload check results
- name: Show unit tests output
if: always()
uses: actions/upload-artifact@main
run: |
find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
shell: bash
- name: Upload artifacts
if: always()
uses: actions/upload-artifact@v2
with:
name: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-artifacts
path: check
name: artifacts-${{ matrix.config.os }}-r${{ matrix.config.r }}
path: AMR.Rcheck

4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 1.7.1.9045
Date: 2021-09-29
Version: 1.7.1.9046
Date: 2021-10-03
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
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@ -1,5 +1,5 @@
# `AMR` 1.7.1.9045
## <small>Last updated: 29 September 2021</small>
# `AMR` 1.7.1.9046
## <small>Last updated: 3 October 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
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4
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">1.7.1.9045</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9046</span>
</span>
</div>
@ -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">29 September 2021</h4>
<h4 data-toc-skip class="date">03 October 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>

12
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">1.7.1.9045</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9046</span>
</span>
</div>
@ -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-1719045" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9045">
<a href="#amr-1719045" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9045</h1>
<div id="last-updated-29-september-2021" class="section level2">
<div id="amr-1719046" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9046">
<a href="#amr-1719046" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9046</h1>
<div id="last-updated-3-october-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>
<a href="#last-updated-3-october-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 3 October 2021</small>
</h2>
<div id="breaking-changes" class="section level3">
<h3 class="hasAnchor">

2
git_development.sh
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@ -127,7 +127,7 @@ echo "••••••••••••••••••••"
echo "• Building package •"
echo "••••••••••••••••••••"
echo "• Building 'data-raw/AMR_latest.tar.gz'..."
Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = TRUE, manual = TRUE, binary = FALSE, quiet = TRUE)"
Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = TRUE, manual = FALSE, binary = FALSE, quiet = TRUE)"
rm data-raw/AMR_latest.tar.gz
mv data-raw/AMR_*.tar.gz data-raw/AMR_latest.tar.gz