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AMR
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(v0.7.1.9103) add lintr to CI

This commit is contained in:
dr. M.S. (Matthijs) Berends 2019-10-11 19:16:49 +02:00
parent 00cdb498a0
commit b2a08d056b
11 changed files with 26 additions and 23 deletions
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22
.gitlab-ci.yml
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@ -19,8 +19,8 @@
# Visit our website for more info: https://msberends.gitlab.io/AMR. # # Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== # # ==================================================================== #
# to check with R-Hub: # to do a full CRAN check with R-Hub:
# chck <- rhub::check_for_cran(devtools::build(args = c('--no-build-vignettes'))) # chck <- rhub::check(devtools::build(), platform = c('debian-clang-devel', 'debian-gcc-devel', 'fedora-clang-devel', 'fedora-gcc-devel', 'windows-x86_64-devel', 'debian-gcc-patched', 'solaris-x86-patched', 'debian-gcc-release', 'windows-x86_64-release', 'macos-elcapitan-release', 'windows-x86_64-oldrel'))
stages: stages:
- build - build
@ -59,7 +59,7 @@ R-release:
script: script:
- Rscript -e 'sessionInfo()' - Rscript -e 'sessionInfo()'
# install missing and outdated packages # install missing and outdated packages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)' - Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE, install_lintr = TRUE)'
# remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file # remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
- rm -rf vignettes - rm -rf vignettes
- Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")' - Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")'
@ -80,11 +80,11 @@ R-release:
R-devel: R-devel:
stage: build stage: build
image: rocker/r-devel image: rocker/r-devel
allow_failure: true allow_failure: false
script: script:
- Rscriptdevel -e 'sessionInfo()' - Rscriptdevel -e 'sessionInfo()'
# install missing and outdated packages # install missing and outdated packages
- Rscriptdevel -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)' - Rscriptdevel -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE)'
# remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file # remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
- rm -rf vignettes - rm -rf vignettes
- Rscriptdevel -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")' - Rscriptdevel -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")'
@ -116,8 +116,6 @@ coverage:
- master - master
script: script:
- apt-get install --yes git - apt-get install --yes git
# install missing and outdated packages
- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = FALSE)'
# codecov token is set in https://gitlab.com/msberends/AMR/settings/ci_cd # codecov token is set in https://gitlab.com/msberends/AMR/settings/ci_cd
- Rscript -e "cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = '$codecov'); cat('Code coverage:', covr::percent_coverage(cc))" - Rscript -e "cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = '$codecov'); cat('Code coverage:', covr::percent_coverage(cc))"
coverage: '/Code coverage: \d+\.\d+/' coverage: '/Code coverage: \d+\.\d+/'
@ -136,8 +134,14 @@ pages:
lintr: lintr:
stage: lint stage: lint
when: on_success when: on_success
cache:
key: r350
paths:
- installed_deps/
policy: pull # no uploading after run
only:
- premaster
- master
script: script:
# install missing and outdated packages
- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = FALSE, install_lintr = TRUE)'
# check all syntax with lintr # check all syntax with lintr
- Rscript -e 'lintr::lint_package()' - Rscript -e 'lintr::lint_package()'

2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 0.7.1.9102 Version: 0.7.1.9103
Date: 2019-10-11 Date: 2019-10-11
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.7.1.9102 # AMR 0.7.1.9103
<small>Last updated: 11-Oct-2019</small> <small>Last updated: 11-Oct-2019</small>
### Breaking ### Breaking

2
docs/404.html
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@ -84,7 +84,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9102</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9103</span>
</span> </span>
</div> </div>

2
docs/LICENSE-text.html
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@ -84,7 +84,7 @@
</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">0.7.1.9102</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9103</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -84,7 +84,7 @@
</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">0.7.1.9102</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9103</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -84,7 +84,7 @@
</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">0.7.1.9102</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9103</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -43,7 +43,7 @@
</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">0.7.1.9102</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9103</span>
</span> </span>
</div> </div>

8
docs/news/index.html
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@ -84,7 +84,7 @@
</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">0.7.1.9102</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9103</span>
</span> </span>
</div> </div>
@ -231,9 +231,9 @@
</div> </div>
<div id="amr-0-7-1-9102" class="section level1"> <div id="amr-0-7-1-9103" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0-7-1-9102" class="anchor"></a>AMR 0.7.1.9102<small> Unreleased </small> <a href="#amr-0-7-1-9103" class="anchor"></a>AMR 0.7.1.9103<small> Unreleased </small>
</h1> </h1>
<p><small>Last updated: 11-Oct-2019</small></p> <p><small>Last updated: 11-Oct-2019</small></p>
<div id="breaking" class="section level3"> <div id="breaking" class="section level3">
@ -1292,7 +1292,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav"> <div id="tocnav">
<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9102">0.7.1.9102</a></li> <li><a href="#amr-0-7-1-9103">0.7.1.9103</a></li>
<li><a href="#amr-0-7-1">0.7.1</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-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li> <li><a href="#amr-0-6-1">0.6.1</a></li>

2
docs/reference/index.html
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@ -84,7 +84,7 @@
</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">0.7.1.9102</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9103</span>
</span> </span>
</div> </div>

3
git_merge.sh
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@ -30,8 +30,7 @@ case "$choice" in
y|Y|j|J ) ;; y|Y|j|J ) ;;
* ) exit 1;; * ) exit 1;;
esac esac
Rscript -e "rhub::check(devtools::build(), platform = c('debian-clang-devel', 'debian-gcc-devel', 'fedora-clang-devel', 'fedora-gcc-devel', 'windows-x86_64-devel', 'debian-gcc-patched', 'solaris-x86-patched', 'debian-gcc-release', 'windows-x86_64-release', 'macos-elcapitan-release', Rscript -e "rhub::check(devtools::build(), platform = c('debian-clang-devel', 'debian-gcc-devel', 'fedora-clang-devel', 'fedora-gcc-devel', 'windows-x86_64-devel', 'debian-gcc-patched', 'solaris-x86-patched', 'debian-gcc-release', 'windows-x86_64-release', 'macos-elcapitan-release', 'windows-x86_64-oldrel'))"
'windows-x86_64-oldrel'))"
echo echo
# and get stashed changes back # and get stashed changes back