Update OmicSelector_create_formula.R #408
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| on: | |
| push: | |
| branches: master | |
| name: R package (Linux) | |
| jobs: | |
| Rpackage: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: OmicSelector | |
| miniconda-version: "latest" | |
| - name: Install enviorment | |
| shell: bash -l {0} | |
| run: | | |
| conda install -c conda-forge conda-pack | |
| sudo apt-get update --fix-missing | |
| sudo chsh -s /bin/bash root && sudo echo 'SHELL=/bin/bash' >> /etc/environment && sudo ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && sudo echo $TZ > /etc/timezone && sudo apt update && sudo apt dist-upgrade -y && sudo apt-get install -y pciutils libkmod-dev libgsl-dev libv8-dev mc libglu1-mesa-dev libgit2-dev gdebi uuid apt-transport-https screen libfontconfig1-dev build-essential libxml2-dev xorg ca-certificates cmake curl git libatlas-base-dev libcurl4-openssl-dev libjemalloc-dev liblapack-dev libopenblas-dev libopencv-dev libzmq3-dev software-properties-common sudo unzip wget && sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test && sudo apt update && sudo apt install -y build-essential libmagick++-dev libbz2-dev libpcre2-16-0 libpcre2-32-0 libpcre2-8-0 libpcre2-dev fort77 xorg-dev liblzma-dev libblas-dev gfortran gcc-multilib gobjc++ libreadline-dev && sudo apt install -y pandoc texinfo texlive-fonts-extra texlive libcairo2-dev freeglut3-dev build-essential libx11-dev libxmu-dev libxi-dev libgl1-mesa-glx libglu1-mesa libglu1-mesa-dev libglfw3-dev libgles2-mesa-dev libopenblas-dev liblapack-dev libopencv-dev build-essential git gcc cmake libcairo2-dev libxml2-dev texlive-full texlive-xetex ttf-mscorefonts-installer build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev default-jre default-jdk && echo "ttf-mscorefonts-installer msttcorefonts/accepted-mscorefonts-eula select true" | debconf-set-selections | |
| sudo apt-get install -y apt-utils libxml2-dev sshfs cifs-utils libffi-dev libx11-dev mesa-common-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libglu1-mesa-dev libssl-dev wget bzip2 ca-certificates build-essential cmake git unzip pkg-config libopenblas-dev liblapack-dev libhdf5-serial-dev libglib2.0-0 libxext6 libsm6 libxrender1 gfortran gcc libglu1-mesa-dev freeglut3-dev mesa-common-dev && sudo apt-get clean | |
| sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 && sudo add-apt-repository -y "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -sc)-cran40/" && sudo apt update && sudo apt -y dist-upgrade && sudo apt install -y r-base-dev texlive-full texlive-xetex ttf-mscorefonts-installer r-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev default-jre default-jdk && sudo chmod 777 -R '/usr/local/lib/R/site-library' && Rscript -e "install.packages(c('remotes','devtools','BiocManager','keras','rgl','rJava'))" | |
| conda create -c anaconda -c conda-forge -n tensorflow tensorflow-gpu keras numpy pandas xgboost scikit-learn tqdm pickle5 | |
| echo 'options(repos = c(CRAN = "https://packagemanager.rstudio.com/cran/latest"));' >> ~/.Rprofile | |
| sudo Rscript -e 'update.packages(ask = F); install.packages(c("devtools","remotes"));' | |
| sudo Rscript -e 'remotes::install_version("RSQLite", version = "2.2.5")' # Temporary fix for RSQLite https://stackoverflow.com/questions/67279457/error-with-r-package-biomart-and-this-dependency-rsqlite | |
| sudo Rscript -e 'devtools::source_url("https://raw.githubusercontent.com/kstawiski/OmicSelector/master/vignettes/setup.R")' | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| TZ: Europe/Warsaw | |
| LANG: C.UTF-8 | |
| LC_ALL: C.UTF-8 | |
| - name: Install package | |
| shell: bash -l {0} | |
| run: | | |
| sudo chmod 777 -R /usr/local/lib/R/site-library/ | |
| sudo R CMD INSTALL . | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Check loading | |
| shell: bash -l {0} | |
| run: | | |
| Rscript -e 'library(OmicSelector); sessionInfo();' | |
| - name: Pack env | |
| shell: bash -l {0} | |
| run: | | |
| conda pack -n OmicSelector -o OmicSelector_conda_pack.tar.gz | |
| mkdir release | |
| mv OmicSelector_conda_pack.tar.gz release/ | |
| split -b 1500M release/OmicSelector_conda_pack.tar.gz "release/OmicSelector_conda_pack.tar.gz.part" | |
| # Removes the latest release, so that we can create a new one in its place | |
| - name: Delete latest release | |
| uses: ame-yu/action-delete-latest-release@v2 | |
| continue-on-error: true # in case there's no existing release | |
| with: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # (optional) Removes the tag associated with the latest release | |
| - name: Delete release tag | |
| run: | | |
| git tag -d release | |
| git push origin :release | |
| continue-on-error: true # in case there's no existing release | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Release | |
| uses: softprops/action-gh-release@v1 | |
| with: | |
| files: | | |
| release/OmicSelector_conda_pack.tar.gz.partaa | |
| release/OmicSelector_conda_pack.tar.gz.partab | |
| release/OmicSelector_conda_pack.tar.gz.partac | |
| release/OmicSelector_conda_pack.tar.gz.partad | |
| body: "OmicSelector - latest version packed as [conda-pack](https://conda.github.io/conda-pack/) and source code. Due to Github limits, the archive is splitted into multiple parts. Use: `cat OmicSelector_conda_pack.tar.gz.part* > OmicSelector_conda_pack.tar.gz` to merge it again." | |
| name: Latest conda-pack (Linux) | |
| tag_name: release | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: 📂 Upload to deploy.konsta.com.pl | |
| uses: SamKirkland/[email protected] | |
| with: | |
| server: konsta.com.pl | |
| username: deploy | |
| password: ${{ secrets.PASSWORD }} | |
| server-dir: ./Deploy/OmicSelector/ | |