Fix deprecated arma::is_finite calls to resolve CRAN warnings #60
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Co-authored-by: gvegayon <893619+gvegayon@users.noreply.github.com>
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[WIP] Fix issues associated with Rcpp
Fix deprecated arma::is_finite calls to resolve CRAN warnings
Sep 29, 2025
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Nov 12, 2025
- 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
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Nov 12, 2025
- 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
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Close as #62 fixes it. |
gvegayon
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Dec 4, 2025
* 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>
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This PR fixes CRAN package check warnings caused by deprecated
arma::is_finite()function calls in the C++ code. The warnings were appearing across multiple R platforms and preventing successful CRAN submission.Issue
CRAN checks were failing with deprecation warnings:
Changes
#include <cmath>header tosrc/infection.cppto supportstd::isfinite()arma::is_finite(times(i))withstd::isfinite(times(i))at two locations:infection_cpp()functionsusceptibility_cpp()functionTesting
sourceCpp()std::isfinite()has identical behavior toarma::is_finite()for finite/NaN/infinite valuesThis minimal change addresses the exact deprecation warnings specified by CRAN and should allow the package to pass all checks for resubmission.
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cloud.r-project.org/usr/lib/R/bin/exec/R -e .libPaths('~/R/library');~+~install.packages(c('Rcpp',~+~'RcppArmadillo'),~+~repos='REDACTED')(dns block)esm.ubuntu.com/usr/lib/apt/methods/https(dns block)If you need me to access, download, or install something from one of these locations, you can either:
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This section details on the original issue you should resolve
<issue_title>Fix issues associated with Rcpp</issue_title>
<issue_description>I recently got this email from CRAN about the R package. We need to fix the issues associated with the changes in the Rcpp package to resubmit the package to CRAN.
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