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(v1.6.0.9004) unit test fix

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dr. M.S. (Matthijs) Berends 2021-04-16 12:02:57 +02:00
parent 00d3e437a8
commit 9842ef9660
15 changed files with 18 additions and 17 deletions
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2
.github/workflows/check.yaml vendored
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@ -65,7 +65,7 @@ jobs:
- {os: ubuntu-20.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.3', allowfail: false rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
# - {os: ubuntu-20.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} # - {os: ubuntu-20.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
# - {os: ubuntu-20.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} # - {os: ubuntu-20.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}

2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.6.0.9003 Version: 1.6.0.9004
Date: 2021-04-16 Date: 2021-04-16
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Authors@R: c( Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.6.0.9003 # AMR 1.6.0.9004
## <small>Last updated: 16 April 2021</small> ## <small>Last updated: 16 April 2021</small>
### New ### New

5
R/aa_helper_functions.R
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@ -217,10 +217,11 @@ is_valid_regex <- function(x) {
FUN = function(y) any(y %in% c("$", "(", ")", "*", "+", "-", FUN = function(y) any(y %in% c("$", "(", ")", "*", "+", "-",
".", "?", "[", "]", "^", "{", ".", "?", "[", "]", "^", "{",
"|", "}", "\\"), "|", "}", "\\"),
na.rm = TRUE)), na.rm = TRUE),
USE.NAMES = FALSE),
error = function(e) rep(TRUE, length(x))) error = function(e) rep(TRUE, length(x)))
regex_valid <- vapply(FUN.VALUE = logical(1), regex_valid <- vapply(FUN.VALUE = logical(1),
X = c("[.", "."), X = x,
FUN = function(y) !"try-error" %in% class(try(grepl(y, ""), FUN = function(y) !"try-error" %in% class(try(grepl(y, ""),
silent = TRUE)), silent = TRUE)),
USE.NAMES = FALSE) USE.NAMES = FALSE)

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R/sysdata.rda
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data-raw/AMR_latest.tar.gz
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2
docs/404.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a> <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">1.6.0.9003</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9004</span>
</span> </span>
</div> </div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</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">1.6.0.9003</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9004</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</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">1.6.0.9003</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9004</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</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">1.6.0.9003</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9004</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -42,7 +42,7 @@
</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">1.6.0.9003</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9004</span>
</span> </span>
</div> </div>

8
docs/news/index.html
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@ -81,7 +81,7 @@
</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">1.6.0.9003</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9004</span>
</span> </span>
</div> </div>
@ -236,9 +236,9 @@
<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-1609003" class="section level1"> <div id="amr-1609004" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9003"> <h1 class="page-header" data-toc-text="1.6.0.9004">
<a href="#amr-1609003" class="anchor"></a>AMR 1.6.0.9003<small> Unreleased </small> <a href="#amr-1609004" class="anchor"></a>AMR 1.6.0.9004<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-16-april-2021" class="section level2"> <div id="last-updated-16-april-2021" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">

2
docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-04-16T09:40Z last_built: 2021-04-16T10:00Z
urls: urls:
reference: https://msberends.github.io/AMR//reference reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles article: https://msberends.github.io/AMR//articles

2
docs/reference/index.html
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@ -81,7 +81,7 @@
</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">1.6.0.9003</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9004</span>
</span> </span>
</div> </div>

2
docs/survey.html
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@ -81,7 +81,7 @@
</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">1.6.0.9003</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9004</span>
</span> </span>
</div> </div>