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AMR
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(v1.6.0.9002) R-3.0 installation fix

This commit is contained in:
dr. M.S. (Matthijs) Berends 2021-04-12 14:24:40 +02:00
parent 6ff5448192
commit d277d58475
17 changed files with 34 additions and 22 deletions
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1
.Rbuildignore
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@ -1,3 +1,4 @@
^.*\.RData$
^.*\.Rproj$
^\.Renviron$
^\.Rprofile$

8
.github/workflows/check.yaml vendored
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@ -66,8 +66,8 @@ jobs:
- {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: '3.3', 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: '3.2', 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: '3.0', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-16.04, r: 'devel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
@ -78,8 +78,8 @@ jobs:
- {os: ubuntu-16.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.3', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
# - {os: ubuntu-16.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
# - {os: ubuntu-16.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.0', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
env:

2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.6.0.9001
Version: 1.6.0.9002
Date: 2021-04-12
Title: Antimicrobial Resistance Data Analysis
Authors@R: c(

3
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.6.0.9001
# AMR 1.6.0.9002
## <small>Last updated: 12 April 2021</small>
### New
@ -13,6 +13,7 @@
* Fix for minor translation errors
* Printing of microbial codes in a `data.frame` or `tibble` now gives a warning if the data contains old microbial codes (from a previous AMR package version)
* `first_isolate()` can now take a vector of values for `col_keyantibiotics` and can have an episode length of `Inf`
* Fixed an installation error on R-3.0
# AMR 1.6.0

11
R/aa_helper_functions.R
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@ -1095,8 +1095,8 @@ time_track <- function(name = NULL) {
paste("(until now:", trimws(round(as.numeric(Sys.time()) * 1000) - pkg_env$time_start), "ms)")
}
# prevent dependency on package 'backports'
# these functions were not available in previous versions of R (last checked: R 4.0.3)
# prevent dependency on package 'backports' ----
# these functions were not available in previous versions of R (last checked: R 4.0.5)
# see here for the full list: https://github.com/r-lib/backports
strrep <- function(x, times) {
x <- as.character(x)
@ -1143,3 +1143,10 @@ isNamespaceLoaded <- function(pkg) {
lengths <- function(x, use.names = TRUE) {
vapply(x, length, FUN.VALUE = NA_integer_, USE.NAMES = use.names)
}
if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.1) {
# R-3.0 does not contain these functions, set them here to prevent installation failure
cospi <- function(...) 1
sinpi <- function(...) 1
tanpi <- function(...) 1
}

1
R/globals.R
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@ -66,6 +66,7 @@ globalVariables(c(".rowid",
"antibiotics",
"atc_group1",
"atc_group2",
"base_ab",
"code",
"cols",
"count",

BIN
data-raw/AMR_latest.tar.gz
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2
docs/404.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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">1.6.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9002</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</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">1.6.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9002</span>
</span>
</div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</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">1.6.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9002</span>
</span>
</div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</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">1.6.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9002</span>
</span>
</div>

2
docs/index.html
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@ -42,7 +42,7 @@
</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">1.6.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9002</span>
</span>
</div>

13
docs/news/index.html
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@ -81,7 +81,7 @@
</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">1.6.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9002</span>
</span>
</div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1609001" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9001">
<a href="#amr-1609001" class="anchor"></a>AMR 1.6.0.9001<small> Unreleased </small>
<div id="amr-1609002" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9002">
<a href="#amr-1609002" class="anchor"></a>AMR 1.6.0.9002<small> Unreleased </small>
</h1>
<div id="last-updated-12-april-2021" class="section level2">
<h2 class="hasAnchor">
@ -270,6 +270,7 @@
<li>
<code><a href="../reference/first_isolate.html">first_isolate()</a></code> can now take a vector of values for <code>col_keyantibiotics</code> and can have an episode length of <code>Inf</code>
</li>
<li>Fixed an installation error on R-3.0</li>
</ul>
</div>
</div>
@ -313,7 +314,7 @@
<span class="co">#&gt; Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
</li>
<li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
<li><p><code>ggplot()</code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
<li>
<p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
@ -370,7 +371,7 @@
<li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
<li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
<li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> on any vector of MIC and disk diffusion values</li>
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
</ul>
</li>
<li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>

2
docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-04-12T10:33Z
last_built: 2021-04-12T12:24Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

2
docs/reference/index.html
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@ -81,7 +81,7 @@
</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">1.6.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9002</span>
</span>
</div>

2
docs/survey.html
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@ -81,7 +81,7 @@
</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">1.6.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9002</span>
</span>
</div>

1
git_premaster.sh
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@ -125,6 +125,7 @@ echo "• Building package •"
echo "••••••••••••••••••••"
echo "• Building 'data-raw/AMR_latest.tar.gz'..."
Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = FALSE, 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
echo "• Installing..."
Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"