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4 changed files with 29 additions and 41 deletions

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@ -95,10 +95,14 @@ jobs:
- uses: r-lib/actions/setup-pandoc@master
- name: Query dependencies
# if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
- name: Install remotes package
if: matrix.config.r != '3.0'
run: |
install.packages('remotes')
shell: Rscript {0}
- name: Query dependencies
run: |
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
shell: Rscript {0}
@ -111,27 +115,15 @@ jobs:
key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-3-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-3-
# - name: Install Linux dependencies
# 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
if: runner.os == 'Linux'
# if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2'
# env:
# RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
# update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
# we don't want to depend on the sysreqs pkg here, as it requires a quite new R version
run: |
sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev
- name: Install package dependencies
# if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
- name: Update package dependencies using remotes package
if: matrix.config.r != '3.0'
run: |
remotes::install_deps(dependencies = TRUE)
shell: Rscript {0}
@ -143,28 +135,8 @@ jobs:
as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
shell: Rscript {0}
# - name: Run R CMD check
# if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
# env:
# _R_CHECK_CRAN_INCOMING_: false
# _R_CHECK_LENGTH_1_CONDITION_: verbose
# _R_CHECK_LENGTH_1_LOGIC2_: verbose
# run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
# shell: Rscript {0}
- name: Unpack AMR package on Linux and macOS
if: runner.os != 'Windows'
run: |
ls -lh
tar -xvf data-raw/AMR_latest.tar.gz
- name: Unpack AMR package on Windows
- name: Run R CMD check on Windows
if: runner.os == 'Windows'
run: |
tar -xvf data-raw/AMR_latest.tar.gz
- name: Run R CMD check
# if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2'
env:
_R_CHECK_CRAN_INCOMING_: false
_R_CHECK_FORCE_SUGGESTS_: false
@ -172,7 +144,22 @@ jobs:
_R_CHECK_LENGTH_1_CONDITION_: verbose
_R_CHECK_LENGTH_1_LOGIC2_: verbose
run: |
R CMD check AMR --no-manual --no-build-vignettes
tar -xf data-raw/AMR_latest.tar.gz
R CMD check AMR -no-manual -as-cran
shell: bash
- name: Run R CMD check on Linux and macOS
if: runner.os != 'Windows'
env:
_R_CHECK_CRAN_INCOMING_: false
_R_CHECK_FORCE_SUGGESTS_: false
_R_CHECK_DEPENDS_ONLY_: true
_R_CHECK_LENGTH_1_CONDITION_: verbose
_R_CHECK_LENGTH_1_LOGIC2_: verbose
run: |
tar -xf data-raw/AMR_latest.tar.gz
R CMD check AMR --no-manual --as-cran
shell: bash
- name: Show testthat output
if: always()

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@ -1,5 +1,5 @@
Package: AMR
Version: 1.6.0.9023
Version: 1.6.0.9025
Date: 2021-05-13
Title: Antimicrobial Resistance Data Analysis
Authors@R: c(

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@ -1,4 +1,4 @@
# `AMR` 1.6.0.9023
# `AMR` 1.6.0.9025
## <small>Last updated: 13 May 2021</small>
### New

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@ -27,6 +27,7 @@
# able to install it. Yet, we want basic R CMD CHECK's in those R versions
# as well, so only run unit tests in later R versions:
if (require("testthat", warn.conflicts = FALSE)) {
library(testthat)
library(AMR)
test_check("AMR")
}