v.0.7.5-alpha #67
Workflow file for this run
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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | |
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
on: | |
release: | |
types: [published] | |
name: test-coverage | |
jobs: | |
test-coverage: | |
runs-on: ubuntu-latest | |
env: | |
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
steps: | |
- uses: actions/checkout@v3 | |
- uses: r-lib/actions/setup-r@v2 | |
with: | |
use-public-rspm: true | |
- uses: r-lib/actions/setup-r-dependencies@v2 | |
with: | |
extra-packages: any::covr | |
needs: coverage | |
- name: Install vsearch | |
run: sudo apt-get install vsearch | |
- name: Install blastn | |
run: sudo apt-get install ncbi-blast+ | |
- name: Install mumu | |
run: | | |
git clone https://github.com/frederic-mahe/mumu.git \ | |
&& cd ./mumu/ \ | |
&& make \ | |
&& make check \ | |
&& sudo make install | |
- name: Install swarm | |
run: | | |
git clone https://github.com/torognes/swarm.git \ | |
&& cd swarm/ \ | |
&& make | |
sudo cp bin/swarm /usr/bin/swarm | |
- name: Install cutadapt | |
run: | | |
sudo python3 -m pip install cutadapt | |
- name: Test coverage | |
run: | | |
covr::codecov( | |
quiet = FALSE, | |
clean = FALSE, | |
install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package") | |
) | |
shell: Rscript {0} | |
- name: Show testthat output | |
if: always() | |
run: | | |
## -------------------------------------------------------------------- | |
find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true | |
shell: bash | |
- name: Upload test results | |
if: failure() | |
uses: actions/upload-artifact@v3 | |
with: | |
name: coverage-test-failures | |
path: ${{ runner.temp }}/package |