remove choices of organism #89
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| name: Test Shiny App Startup | |
| on: [push] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| env: | |
| RENV_PATHS_ROOT: ~/.cache/R/renv | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 4.2.0 | |
| - name: Restore Renv package cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| ${{ env.RENV_PATHS_ROOT }} | |
| ./renv/library | |
| key: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{ inputs.cache-version }}-${{ hashFiles('renv.lock') }} | |
| restore-keys: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{ inputs.cache-version }}- | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev libsqlite3-dev libglu1-mesa-dev default-jdk libmagick++-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev | |
| sudo apt install curl | |
| - name: Install and activate renv | |
| shell: Rscript {0} | |
| run: | | |
| install.packages("renv") | |
| renv::restore() | |
| # - name: Get R and OS version | |
| # id: get-version | |
| # run: | | |
| # cat("##[set-output name=os-version;]", sessionInfo()$running, "\n", sep = "") | |
| # cat("##[set-output name=r-version;]", R.Version()$version.string, sep = "") | |
| # shell: Rscript {0} | |
| # - name: Setup renv | |
| # uses: r-lib/actions/setup-renv@v2 | |
| # - name: Restore packages | |
| # shell: Rscript {0} | |
| # run: | | |
| # renv::restore() | |
| # - name: test specific packages | |
| # run: | | |
| # Rscript -e 'install.packages("Rcpp")' | |
| # Rscript -e 'install.packages("RcppArmadillo")' | |
| # Rscript -e 'install.packages("DESeq2")' | |
| - name: Test if Shiny app starts | |
| timeout-minutes: 2 | |
| shell: Rscript {0} | |
| run: | | |
| install.packages('processx') | |
| library(processx) | |
| execute_shiny_app <- function() { | |
| tryCatch( | |
| { | |
| # Start the Shiny app in a separate process | |
| app_process <- process$new( | |
| "Rscript", | |
| c("-e", "shiny::runApp('program/shinyApp', launch.browser = FALSE, port = 3838)"), | |
| stdout = "|", stderr = "|" | |
| ) | |
| # Wait for a few seconds to allow the app to start | |
| Sys.sleep(15) | |
| # Check if the process is still running | |
| if (app_process$is_alive()) { | |
| # Terminate the app if it started successfully | |
| app_process$kill() | |
| return("Success") | |
| } else { | |
| # Capture and return the error message if the app failed to start | |
| error_message <- app_process$read_error() | |
| return(paste("Error:", error_message)) | |
| } | |
| }, | |
| error = function(e) { | |
| return(paste("Error:", e$message)) | |
| } | |
| ) | |
| } | |
| result <- execute_shiny_app() | |
| # Check if the result is "failure" | |
| if (result == "Success") { | |
| cat("Test passed") | |
| } else { | |
| cat("Test failed: Output is 'failure'\n") | |
| quit(status = 1) | |
| } | |
| - name: Save cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| ~/.local/share/renv | |
| ./renv/library | |
| key: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{ inputs.cache-version }}-${{ hashFiles('renv.lock') }} | |