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aoliveramCopilotgvegayon
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Fix GitHub Actions Ubuntu runner libssl.so.3.1 error (#62)
* Initial plan * Replace deprecated arma::is_finite with std::isfinite Co-authored-by: gvegayon <893619+gvegayon@users.noreply.github.com> * Fix GitHub Actions Ubuntu runner libssl issue - Update RSPM URLs from focal (20.04) to noble (24.04) - Explicitly install libssl-dev and libcurl4-openssl-dev - Update system_requirements() to target Ubuntu 24.04 - Fixes ubuntu-latest (release) check failure with libssl.so.3.1 Resolves #60 * Add missing system dependencies for igraph - Install libglpk-dev (required by igraph) - Install libgmp3-dev and libxml2-dev (additional dependencies) - Update local check script to include knitr - Fixes igraph.so loading error in GitHub Actions Related to #60 * Switch GitHub Actions to modern r-lib actions (#63) * Initial plan * Switch to modern r-lib actions and add scripts to .Rbuildignore Co-authored-by: gvegayon <893619+gvegayon@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: gvegayon <893619+gvegayon@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: gvegayon <893619+gvegayon@users.noreply.github.com>
1 parent f656013 commit aeea532

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‎.Rbuildignore‎

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@@ -40,4 +40,5 @@ makefile
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^\.github
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netdiffuseR\.Rcheck
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^\.devcontainer$
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^\.vscode$
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^\.vscode$
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^scripts$

‎.github/workflows/r.yml‎

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# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
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# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches:
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- main
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- master
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branches: [main, master]
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pull_request:
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branches:
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- main
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- master
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branches: [main, master]
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name: R-CMD-check
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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jobs:
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R-CMD-check:
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runs-on: ${{ matrix.config.os }}
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fail-fast: false
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matrix:
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config:
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- {os: macOS-latest, r: 'release'}
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- {os: windows-latest, r: 'release'}
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- {os: macOS-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-latest, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-latest, r: 'devel', valgrind: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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- {os: ubuntu-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'devel', valgrind: true, http-user-agent: 'release'}
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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RSPM: ${{ matrix.config.rspm }}
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- uses: r-lib/actions/setup-pandoc@v2
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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shell: Rscript {0}
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- name: Restore R package cache
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if: runner.os != 'Windows'
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uses: actions/cache@v4
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
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- name: Install system dependencies
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if: runner.os == 'Linux'
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run: |
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while read -r cmd
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do
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eval sudo $cmd
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done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
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- name: Install dependencies
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run: |
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remotes::install_deps(dependencies = TRUE)
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remotes::install_cran("rcmdcheck")
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shell: Rscript {0}
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extra-packages: any::rcmdcheck
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needs: check
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- name: Check
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- uses: r-lib/actions/check-r-package@v2
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if: ${{ matrix.config.valgrind != true }}
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env:
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_R_CHECK_CRAN_INCOMING_REMOTE_: false
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run: |
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options(crayon.enabled = TRUE)
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rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
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shell: Rscript {0}
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with:
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args: 'c("--no-manual", "--as-cran")'
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upload-snapshots: false
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upload-results: false
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check-dir: '"check"'
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error-on: '"error"'
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- name: Setup valgrind
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if: ${{ matrix.config.valgrind == true }}

‎scripts/check-github-actions-local.sh‎

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#!/usr/bin/env bash
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#
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# check-github-actions-local.sh - Simulate GitHub Actions checks locally
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#
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# This script replicates the GitHub Actions workflow locally using Docker
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# to test changes before pushing to GitHub.
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#
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# Usage:
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# ./scripts/check-github-actions-local.sh [ubuntu|macos|windows|all]
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#
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# Requirements:
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# - Docker installed and running
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# - Run from repository root
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set -e
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set -u
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# Colors
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RED='\033[0;31m'
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GREEN='\033[0;32m'
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YELLOW='\033[1;33m'
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BLUE='\033[0;34m'
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NC='\033[0m'
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# Configuration
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PLATFORM="${1:-ubuntu}"
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PACKAGE_NAME=$(awk '/^Package:/ {print $2}' DESCRIPTION)
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PACKAGE_VERSION=$(awk '/^Version:/ {print $2}' DESCRIPTION)
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echo -e "${GREEN}========================================${NC}"
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echo -e "${GREEN}GitHub Actions Local Check${NC}"
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echo -e "${GREEN}========================================${NC}"
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echo "Package: ${PACKAGE_NAME} ${PACKAGE_VERSION}"
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echo "Platform: ${PLATFORM}"
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echo ""
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case "$PLATFORM" in
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ubuntu|linux)
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echo -e "${YELLOW}[1/3] Testing Ubuntu (r-release)...${NC}"
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# Use R-hub Ubuntu container (simulates ubuntu-latest with R release)
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docker run --rm \
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-v "$(pwd):/workspace" \
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-w /workspace \
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ghcr.io/r-hub/containers/ubuntu-release:latest \
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bash -c "
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set -e
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echo '>>> Installing system dependencies...'
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apt-get update > /dev/null 2>&1
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apt-get install -y libssl-dev libcurl4-openssl-dev libglpk-dev libgmp3-dev libxml2-dev > /dev/null 2>&1
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echo '>>> Installing R package dependencies...'
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Rscript -e \"install.packages(c('Rcpp', 'RcppArmadillo', 'sna', 'network', 'networkDynamic', 'Matrix', 'MASS', 'MatchIt', 'SparseM', 'boot', 'igraph', 'viridisLite', 'rcmdcheck', 'remotes', 'knitr'), repos='https://packagemanager.posit.co/cran/__linux__/noble/latest', quiet=TRUE)\"
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echo '>>> Running R CMD check...'
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Rscript -e \"rcmdcheck::rcmdcheck(args = c('--no-manual', '--as-cran'), error_on = 'warning', check_dir = 'check')\"
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" && echo -e "${GREEN}✓ Ubuntu check passed${NC}" || echo -e "${RED}✗ Ubuntu check failed${NC}"
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;;
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macos|mac)
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echo -e "${YELLOW}macOS checks require macOS host - skipped${NC}"
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echo "To test on macOS, run: R CMD build . && R CMD check --as-cran *.tar.gz"
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;;
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windows|win)
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echo -e "${YELLOW}Windows checks require Windows host - skipped${NC}"
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echo "To test on Windows, use rhub or GitHub Actions"
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;;
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all)
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echo -e "${BLUE}Running all available checks...${NC}"
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$0 ubuntu
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;;
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*)
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echo -e "${RED}Unknown platform: $PLATFORM${NC}"
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echo "Usage: $0 [ubuntu|macos|windows|all]"
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exit 1
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;;
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esac
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echo ""
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echo -e "${GREEN}========================================${NC}"
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echo -e "${GREEN}Local check completed!${NC}"
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echo -e "${GREEN}========================================${NC}"
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echo ""
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echo "Note: This simulates GitHub Actions but may have minor differences."
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echo "For exact GitHub Actions behavior, push to a branch and create a PR."
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echo ""

‎src/infection.cpp‎

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// [[Rcpp::depends(RcppArmadillo)]]
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#include <RcppArmadillo.h>
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#include <cmath>
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using namespace Rcpp;
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// [[Rcpp::export]]
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Rcpp::checkUserInterrupt();
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// If NA (aka nan in Armadillo), then NA.
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if (!arma::is_finite(times(i))) {
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if (!std::isfinite(times(i))) {
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infect.at(i) = NA_REAL;
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continue;
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}
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Rcpp::checkUserInterrupt();
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// If NA (aka nan in Armadillo), then NA.
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if (!arma::is_finite(times(i))) {
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if (!std::isfinite(times(i))) {
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suscep.at(i) = NA_REAL;
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continue;
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}

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