Fix clang compiler bug for CRAN submission (#75)

* Update DESCRIPTION with minimum version of R * Update with latest from C++ library * Bump version number * Update NEWS.md * Update NEWS.md * Update CITATION * Update GHA to use macOS 13 * Revert to macos latest
UofUEpiBio · Jan 28, 2025 · af9b8ec · af9b8ec
1 parent 30afdce
commit af9b8ec
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Showing 6 changed files with 34 additions and 13 deletions.
diff --git a/.github/workflows/r.yml b/.github/workflows/r.yml
@@ -31,9 +31,9 @@ jobs:
           - {os: macOS-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: windows-latest, r: 'devel', http-user-agent: 'release'}
           # se older ubuntu to maximise backward compatibility
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -65,7 +65,7 @@ jobs:
           error-on: '"warning"'
 
       - uses: r-lib/actions/check-r-package@v2
-        if: ${{ matrix.config.os != 'ubuntu-latest' || matrix.config.r != 're;ease' }}
+        if: ${{ matrix.config.os != 'ubuntu-latest' || matrix.config.r != 'release' }}
         with:
           upload-snapshots: false
           upload-results: false

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,8 @@
 Package: epiworldR
 Type: Package
 Title: Fast Agent-Based Epi Models
-Version: 0.6.0.0
+Version: 0.6.1.0
+Depends: R (>= 4.1.0)
 Authors@R: c(
   person(given="George", family="Vega Yon", role=c("aut"),
   email="g.vegayon@gmail.com", comment = c(ORCID = "0000-0002-3171-0844")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,11 @@
-# epiworldR 0.6.0.0
+# epiworldR 0.6.1.0
+
+* Updates to reflect changes in the `epiworld` C++ library (mostly bug fixes)
+
+* Package now requires R version >=4.1.0, because it uses the pipe `|>`
 
-## New features
+
+# epiworldR 0.6.0.0
 
 * The package now includes the `LFMCMC` module that implements
   the likelihood-free Markov Chain Monte Carlo algorithm. This
@@ -15,8 +20,6 @@
 * The function `today()` returns the current day (step) of the
   simulation.
 
-## Misc
-
 * We changed the versioning system. To allow the R package to increase
   version number while preserving epiworld (C++) versioning, we added a fourth
   number that indicates R-only patches (similar to RcppArmadillo).

diff --git a/inst/CITATION b/inst/CITATION
@@ -1,4 +1,4 @@
-year <- 2024
+year <- 2025
 note <- sprintf("R package version %s", meta$Version)
 
 bibentry(

diff --git a/inst/include/epiworld/epiworld.hpp b/inst/include/epiworld/epiworld.hpp
@@ -19,7 +19,7 @@
 /* Versioning */
 #define EPIWORLD_VERSION_MAJOR 0
 #define EPIWORLD_VERSION_MINOR 6
-#define EPIWORLD_VERSION_PATCH 0
+#define EPIWORLD_VERSION_PATCH 1
 
 static const int epiworld_version_major = EPIWORLD_VERSION_MAJOR;
 static const int epiworld_version_minor = EPIWORLD_VERSION_MINOR;

diff --git a/inst/include/epiworld/math/lfmcmc/lfmcmc-meat-print.hpp b/inst/include/epiworld/math/lfmcmc/lfmcmc-meat-print.hpp
@@ -93,7 +93,16 @@ inline void LFMCMC<TData>::print(size_t burnin) const
     for (auto & n : summ_params)
     {
 
-        int tmp_nchar = std::floor(std::log10(std::abs(n)));
+        int tmp_nchar;
+
+        if (std::abs(n) < 1) {
+            // std::log10(<1) will return negative number
+            // std::log10(0) will return -inf and throw a runtime error
+            tmp_nchar = 0;
+        } else {
+            tmp_nchar = std::floor(std::log10(std::abs(n)));
+        }
+
         if (nchar_par_num < tmp_nchar)
             nchar_par_num = tmp_nchar;
     }
@@ -161,7 +170,15 @@ inline void LFMCMC<TData>::print(size_t burnin) const
     int nchar = 0;
     for (auto & s : summ_stats)
     {
-        int tmp_nchar = std::floor(std::log10(std::abs(s)));
+        int tmp_nchar;
+        if (std::abs(s) < 1) {
+            // std::log10(<1) will return negative number
+            // std::log10(0) will return -inf and throw a runtime error
+            tmp_nchar = 0;
+        } else {
+            tmp_nchar = std::floor(std::log10(std::abs(s)));
+        }
+
         if (nchar < tmp_nchar)
             nchar = tmp_nchar;
     }