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(v1.4.0.9058) GH actions update

This commit is contained in:
dr. M.S. (Matthijs) Berends 2021-01-04 11:27:37 +01:00
parent daac96fefe
commit 82cfa24ea4
13 changed files with 40 additions and 36 deletions
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48
.github/workflows/check.yaml vendored
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@ -56,6 +56,10 @@ jobs:
- {os: windows-latest, r: 'devel', allowfail: false} - {os: windows-latest, r: 'devel', allowfail: false}
- {os: windows-latest, r: 'release', allowfail: false} - {os: windows-latest, r: 'release', allowfail: false}
- {os: windows-latest, r: 'oldrel', allowfail: false} - {os: windows-latest, r: 'oldrel', allowfail: false}
- {os: ubuntu-20.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: 'release', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: 'oldrel', 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"} - {os: ubuntu-16.04, r: 'devel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: 'oldrel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: 'oldrel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
@ -67,12 +71,6 @@ jobs:
- {os: ubuntu-16.04, r: '3.2', 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: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-20.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: 'release', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: 'oldrel', 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"}
env: env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@ -95,7 +93,7 @@ jobs:
shell: Rscript {0} shell: Rscript {0}
- name: Cache R packages - name: Cache R packages
if: runner.os != 'Windows' if: runner.os != 'Windows' && matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
uses: actions/cache@v1 uses: actions/cache@v1
with: with:
path: ${{ env.R_LIBS_USER }} path: ${{ env.R_LIBS_USER }}
@ -103,7 +101,16 @@ jobs:
restore-keys: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-3- restore-keys: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-3-
- name: Install Linux dependencies - name: Install Linux dependencies
if: runner.os == 'Linux' if: runner.os == 'Linux' && matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
env:
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
run: |
Rscript -e "remotes::install_github('r-hub/sysreqs')"
sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
sudo -s eval "$sysreqs"
- name: Install Linux dependencies on old R versions
if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2'
env: env:
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
# update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu). # update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
@ -117,8 +124,10 @@ jobs:
brew install mariadb-connector-c brew install mariadb-connector-c
- name: Install dependencies - name: Install dependencies
if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
run: | run: |
utils::update.packages(ask = FALSE) remotes::install_deps(dependencies = TRUE)
remotes::install_cran("rcmdcheck")
shell: Rscript {0} shell: Rscript {0}
- name: Session info - name: Session info
@ -128,32 +137,27 @@ jobs:
as.data.frame(utils::installed.packages())[, "Version", drop = FALSE] as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
shell: Rscript {0} shell: Rscript {0}
- name: Run R CMD check # - name: Run R CMD check
if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2' # if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
env: # env:
_R_CHECK_CRAN_INCOMING_: false # _R_CHECK_CRAN_INCOMING_: false
run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") # run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
shell: Rscript {0} # shell: Rscript {0}
- name: Run R CMD check on older R versions - name: Run R CMD check on older R versions
if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2' # if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2'
env: env:
_R_CHECK_CRAN_INCOMING_: false _R_CHECK_CRAN_INCOMING_: false
_R_CHECK_FORCE_SUGGESTS_: false _R_CHECK_FORCE_SUGGESTS_: false
# these are set already in --as-cran:
_R_CHECK_LENGTH_1_CONDITION_: verbose _R_CHECK_LENGTH_1_CONDITION_: verbose
_R_CHECK_LENGTH_1_LOGIC2_: verbose _R_CHECK_LENGTH_1_LOGIC2_: verbose
run: | run: |
R CMD check data-raw/AMR_*.tar.gz --no-manual R CMD check data-raw/AMR_*.tar.gz --no-manual --as-cran
- name: Show testthat output - name: Show testthat output
if: always() if: always()
run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
shell: bash shell: bash
- name: Install packages to check for new deps
run: |
R CMD INSTALL data-raw/AMR_*.tar.gz
- name: Upload check results - name: Upload check results
if: failure() if: failure()

2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.4.0.9057 Version: 1.4.0.9058
Date: 2021-01-04 Date: 2021-01-04
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 1.4.0.9057 # AMR 1.4.0.9058
## <small>Last updated: 4 January 2021</small> ## <small>Last updated: 4 January 2021</small>
### New ### New
* Functions `get_episode()` and `is_new_episode()` to determine (patient) episodes which are not necessarily based on microorganisms. The `get_episode()` function returns the index number of the episode per group, while the `is_new_episode()` function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode. They also support `dplyr`s grouping (i.e. using `group_by()`): * Functions `get_episode()` and `is_new_episode()` to determine (patient) episodes which are not necessarily based on microorganisms. The `get_episode()` function returns the index number of the episode per group, while the `is_new_episode()` function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode. They also support `dplyr`s grouping (i.e. using `group_by()`):

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data-raw/AMR_1.4.0.9057.tar.gz → data-raw/AMR_1.4.0.9058.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">1.4.0.9057</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</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">1.4.0.9057</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</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">1.4.0.9057</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</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">1.4.0.9057</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</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">1.4.0.9057</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</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">1.4.0.9057</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</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-1409057" class="section level1"> <div id="amr-1409058" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9057"> <h1 class="page-header" data-toc-text="1.4.0.9058">
<a href="#amr-1409057" class="anchor"></a>AMR 1.4.0.9057<small> Unreleased </small> <a href="#amr-1409058" class="anchor"></a>AMR 1.4.0.9058<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-4-january-2021" class="section level2"> <div id="last-updated-4-january-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: 2021-01-04T08:49Z last_built: 2021-01-04T10:27Z
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">1.4.0.9057</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</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">1.4.0.9057</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span>
</span> </span>
</div> </div>