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remove reduntant dependency install
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katosh committed Jun 18, 2024
1 parent eaa4526 commit 47c84ec
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37 changes: 0 additions & 37 deletions .github/workflows/R-CMD-check.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -27,43 +27,6 @@ jobs:
with:
extra-packages: any::covr, any::xml2

- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: '3.8'

- name: Install system dependencies
run: |
sudo apt-get update
sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev libharfbuzz-dev libfribidi-dev libfontconfig1-dev libpng-dev pandoc pandoc-citeproc
- name: Install Python dependencies
run: |
python -m pip install --upgrade pip
pip install anndata
pip install numpy
env:
RETICULATE_PYTHON: /opt/hostedtoolcache/Python/3.8.10/x64/bin/python

- name: Verify Python installation
run: |
which python
python --version
pip list
- name: Install Bioconductor packages
run: |
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install(c("SingleCellExperiment", "SummarizedExperiment", "S4Vectors", "BiocNeighbors"))
shell: Rscript {0}

- name: Install R package dependencies
run: |
install.packages('remotes')
install.packages('devtools')
remotes::install_deps(dependencies = TRUE)
shell: Rscript {0}

- name: Install package
run: |
remotes::install_local()
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