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AMR
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(v1.7.1.9029) unit test fix

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dr. M.S. (Matthijs) Berends 2021-08-21 10:20:05 +02:00
parent e4de7f5055
commit f0a4d29fe0
6 changed files with 19 additions and 14 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.7.1.9028 Version: 1.7.1.9029
Date: 2021-08-20 Date: 2021-08-21
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by

4
NEWS.md
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# `AMR` 1.7.1.9028 # `AMR` 1.7.1.9029
## <small>Last updated: 20 August 2021</small> ## <small>Last updated: 21 August 2021</small>
### Breaking changes ### Breaking changes
* Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version * Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version

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data-raw/_install_deps.R
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@ -39,7 +39,11 @@ if (length(to_install) == 0) {
} }
for (i in seq_len(length(to_install))) { for (i in seq_len(length(to_install))) {
cat("Installing package", to_install[i], "\n") cat("Installing package", to_install[i], "\n")
tryCatch(install.packages(to_install[i], repos = "https://cran.rstudio.com/", dependencies = c("Depends", "Imports"), quiet = FALSE), tryCatch(install.packages(to_install[i],
type = ifelse(.Platform$OS.type == "unix", "source", "binary"),
repos = "https://cran.rstudio.com/",
dependencies = c("Depends", "Imports"),
quiet = FALSE),
# message = function(m) invisible(), # message = function(m) invisible(),
warning = function(w) message(w$message), warning = function(w) message(w$message),
error = function(e) message(e$message)) error = function(e) message(e$message))
@ -51,9 +55,10 @@ if (length(to_update) == 0) {
message("\nNothing to update\n") message("\nNothing to update\n")
} }
for (i in seq_len(length(to_update))) { for (i in seq_len(length(to_update))) {
cat("Updating package", to_update[i], "\n") cat("Updating package '", to_update[i], "' v", as.character(packageVersion(to_update[i])), "\n", sep = "")
tryCatch(update.packages(to_update[i], repos = "https://cran.rstudio.com/", ask = FALSE), tryCatch(update.packages(to_update[i], repos = "https://cran.rstudio.com/", ask = FALSE),
# message = function(m) invisible(), # message = function(m) invisible(),
warning = function(w) message(w$message), warning = function(w) message(w$message),
error = function(e) message(e$message)) error = function(e) message(e$message))
cat("Updated to '", to_update[i], "' v", as.character(packageVersion(to_update[i])), "\n", sep = "")
} }

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docs/articles/datasets.html
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@ -44,7 +44,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.7.1.9028</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9029</span>
</span> </span>
</div> </div>
@ -190,7 +190,7 @@
<div class="page-header toc-ignore"> <div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1> <h1 data-toc-skip>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">20 August 2021</h4> <h4 data-toc-skip class="date">21 August 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> <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> <div class="hidden name"><code>datasets.Rmd</code></div>

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docs/news/index.html
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@ -92,7 +92,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.7.1.9028</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9029</span>
</span> </span>
</div> </div>
@ -240,12 +240,12 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1719028" class="section level1"> <div id="amr-1719029" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9028"> <h1 class="page-header" data-toc-text="1.7.1.9029">
<a href="#amr-1719028" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9028</h1> <a href="#amr-1719029" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9029</h1>
<div id="last-updated-20-august-2021" class="section level2"> <div id="last-updated-21-august-2021" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-20-august-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 20 August 2021</small> <a href="#last-updated-21-august-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 21 August 2021</small>
</h2> </h2>
<div id="breaking-changes" class="section level3"> <div id="breaking-changes" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">