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deal with corncob not being on CRAN #62

deal with corncob not being on CRAN

deal with corncob not being on CRAN #62

Workflow file for this run

# 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:
push:
branches: [main, master]
pull_request:
branches: [main, master]
name: R-CMD-check
jobs:
R-CMD-check:
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.r }})
strategy:
fail-fast: false
matrix:
config:
- {os: ubuntu-latest, r: 'release'}
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
R_KEEP_PKG_SOURCE: yes
steps:
- uses: actions/checkout@v2
- uses: r-lib/actions/setup-pandoc@v2
- uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
http-user-agent: ${{ matrix.config.http-user-agent }}
use-public-rspm: true
- name: "Install libraries"
run: |
sudo apt-get update
sudo apt-get install -y git bzip2 \
cmake autoconf automake make gcc perl zlib1g-dev libbz2-dev samtools
- name: "Install aligners and SLIMM"
run: |
rm -rf vignettes
curl -L https://github.com/lh3/minimap2/releases/download/v2.13/minimap2-2.13_x64-linux.tar.bz2 | tar -jxf -
sudo cp ./minimap2-2.13_x64-linux/minimap2 /usr/bin/ && rm -rf ./minimap2-*
git clone --recursive https://github.com/seqan/slimm
(cd slimm && mkdir build && cd build && cmake .. && make && sudo cp bin/slimm /usr/bin/)
rm -rf slimm
- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: any::rcmdcheck, any::XML
needs: check
- uses: r-lib/actions/check-r-package@v2