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AMR
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(v0.7.1.9019) CI fix

This commit is contained in:
dr. M.S. (Matthijs) Berends 2019-07-30 19:20:13 +02:00
parent 2a62c3d62a
commit a6606d334c
11 changed files with 14 additions and 14 deletions
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2
.gitlab-ci.yml
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@ -118,7 +118,7 @@ coverage:
# install missing and outdated packages
- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)'
# codecov token is set in https://gitlab.com/msberends/AMR/settings/ci_cd
- Rscript -e "cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = '$codecov', exclusions = c('R/atc_online.R', 'R/mo_source.R')); cat('Code coverage:', covr::percent_coverage(cc))"
- Rscript -e "cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = '$codecov', exclusions = c('R/atc_online.R', 'R/mo_source.R', 'R/resistance_predict.R')); cat('Code coverage:', covr::percent_coverage(cc))"
coverage: '/Code coverage: \d+\.\d+/'
pages:

2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 0.7.1.9018
Version: 0.7.1.9019
Date: 2019-07-30
Title: Antimicrobial Resistance Analysis
Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.7.1.9018
# AMR 0.7.1.9019
### Breaking
* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. We decided to create a new package for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.

2
appveyor.yml
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@ -39,7 +39,7 @@ environment:
GCC_PATH: mingw_64
WARNINGS_ARE_ERRORS: 1
PKGTYPE: win.binary
# USE_RTOOLS: true
USE_RTOOLS: true
matrix:
- R_VERSION: release

2
docs/LICENSE-text.html
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@ -78,7 +78,7 @@
</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">0.7.1.9018</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9019</span>
</span>
</div>

2
docs/articles/index.html
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@ -78,7 +78,7 @@
</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">0.7.1.9018</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9019</span>
</span>
</div>

2
docs/authors.html
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@ -78,7 +78,7 @@
</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">0.7.1.9018</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9019</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">0.7.1.9018</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9019</span>
</span>
</div>

8
docs/news/index.html
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@ -78,7 +78,7 @@
</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">0.7.1.9018</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9019</span>
</span>
</div>
@ -225,9 +225,9 @@
</div>
<div id="amr-0-7-1-9018" class="section level1">
<div id="amr-0-7-1-9019" class="section level1">
<h1 class="page-header">
<a href="#amr-0-7-1-9018" class="anchor"></a>AMR 0.7.1.9018<small> Unreleased </small>
<a href="#amr-0-7-1-9019" class="anchor"></a>AMR 0.7.1.9019<small> Unreleased </small>
</h1>
<div id="breaking" class="section level3">
<h3 class="hasAnchor">
@ -1198,7 +1198,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9018">0.7.1.9018</a></li>
<li><a href="#amr-0-7-1-9019">0.7.1.9019</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li>

2
docs/reference/index.html
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@ -78,7 +78,7 @@
</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">0.7.1.9018</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9019</span>
</span>
</div>

2
git_premaster.sh
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@ -36,7 +36,7 @@ fi
sed -i -- "s/^Version: .*/Version: ${new_version}/" DESCRIPTION
# update 1st line of NEWS.md
sed -i -- "1s/.*/# AMR ${new_version}/" NEWS.md
rm *--
rm *-- || true
echo "• First 3 lines of DESCRIPTION:"
head -3 DESCRIPTION
echo