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(v1.6.0.9023) new unit test flow

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dr. M.S. (Matthijs) Berends
2021-05-13 19:31:47 +02:00
parent 655b813e99
commit aeea00881e
34 changed files with 408 additions and 355 deletions
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70
.github/workflows/check.yaml vendored
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@ -96,48 +96,44 @@ 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'
# if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
shell: Rscript {0}
- name: Cache R packages
if: runner.os != 'Windows' && matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
if: runner.os != 'Windows'
# && matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
uses: actions/cache@v1
with:
path: ${{ env.R_LIBS_USER }}
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' && 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:
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
- 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 macOS dependencies
if: matrix.config.os == 'macOS-latest' && matrix.config.r == 'devel'
run: |
brew install mariadb-connector-c
- name: Install package dependencies
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'
run: |
remotes::install_deps(dependencies = TRUE)
remotes::install_cran("rcmdcheck")
shell: Rscript {0}
- name: Session info
@ -147,17 +143,28 @@ 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: 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
if: runner.os == 'Windows'
run: |
tar -xvf data-raw/AMR_latest.tar.gz
- 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'
- 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
@ -165,7 +172,6 @@ jobs:
_R_CHECK_LENGTH_1_CONDITION_: verbose
_R_CHECK_LENGTH_1_LOGIC2_: verbose
run: |
tar -xvf data-raw/AMR_latest.tar.gz
R CMD check AMR --no-manual --no-build-vignettes
- name: Show testthat output