Fix CRAN pre-test issues: VLA warnings, obsolete C++11, bump to v1.1.1

- Replace C++ variable length arrays with std::vector<double> (3 sites)
- Remove CXX_STD=CXX11 from Makevars/Makevars.win and C++11 from SystemRequirements
- Remove LAPACK/BLAS double-link flags from Makevars (macOS Abort trap fix)
- Update cran-comments.md with resubmission notes

Author: timktsang

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: seroreconstruct
 Type: Package
 Title: Reconstructing Antibody Dynamics to Estimate the Risk of Influenza Virus Infection
-Version: 1.1.0
+Version: 1.1.1
 Authors@R: 
     c(person(given = "Tim",
              family = "Tsang",
@@ -34,5 +34,5 @@ Suggests:
     rmarkdown
 Config/testthat/edition: 3
 VignetteBuilder: knitr
-SystemRequirements: C++11, TBB
+SystemRequirements: TBB
 RoxygenNote: 7.3.3

NEWS.md

@@ -1,3 +1,15 @@
+# seroreconstruct 1.1.1
+
+## Bug fixes
+
+* Fixed variable length array (VLA) warnings in C++ code flagged by GCC 14
+  on Windows (`-Wvla`). Replaced with `std::vector<double>`.
+
+* Removed obsolete `CXX_STD = CXX11` from Makevars files and
+  `SystemRequirements` — the default C++ standard is sufficient.
+
+---
+
 # seroreconstruct 1.1.0
 
 ## New features

cran-comments.md

@@ -1,4 +1,12 @@
-# CRAN submission comments — seroreconstruct 1.1.0
+# CRAN submission comments — seroreconstruct 1.1.1
+
+## Resubmission
+
+This is a resubmission addressing CRAN pre-test feedback on v1.1.0:
+
+- **Fixed**: Variable Length Arrays (VLA) in C++ replaced with `std::vector<double>` (3 occurrences in `mcmc_function.cpp`). This resolves the `-Wvla` warning on Windows/GCC.
+- **Fixed**: Removed obsolete `CXX_STD = CXX11` from `Makevars` and `Makevars.win`, and removed `C++11` from `SystemRequirements`. The package compiles fine under the default C++ standard.
+- **Noted**: "Misspelled" words (HAI, Tsang, et, al, titer) are all correct — HAI is a standard immunology abbreviation (hemagglutination inhibition), titer is the standard US English spelling, and Tsang et al. is an author citation.
 
 ## R CMD check results
 

src/Makevars

@@ -1,2 +1 @@
-CXX_STD = CXX11
-PKG_LIBS = `"$(R_HOME)/bin/Rscript" -e "RcppParallel::RcppParallelLibs()"` $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+PKG_LIBS = `"$(R_HOME)/bin/Rscript" -e "RcppParallel::RcppParallelLibs()"`

src/Makevars.win

@@ -1,3 +1,2 @@
-CXX_STD = CXX11
 PKG_CXXFLAGS = -DRCPP_PARALLEL_USE_TBB=1
 PKG_LIBS = $(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "RcppParallel::RcppParallelLibs()") $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

src/mcmc_function.cpp

@@ -509,7 +509,7 @@ double proratio=0;
 if (ifupdate[1]==1){	
 int problength=data111(b1,4);
 
-double prob[problength];
+std::vector<double> prob(problength);
 double totalprob=0;
 
 for (b2=problength-1;b2>=data111(b1,3);--b2){
@@ -863,7 +863,7 @@ data21pro(b1,6)=R::rgamma(para[19+4*(data11(b1,13))+2*data11(b1,14)],1.0);
 // infection time
 int problength=data111(b1,4);
 
-double prob[problength];
+std::vector<double> prob(problength);
 double totalprob=0;
 
 for (b2=problength-1;b2>=data111(b1,3);--b2){
@@ -1084,7 +1084,7 @@ data21pro(b1,6)=R::rgamma(para[19+4*(data11(b1,13))+2*data11(b1,14)],1.0);
 // infection time
 int problength=data111(b1,4);
 
-double prob[problength];
+std::vector<double> prob(problength);
 double totalprob=0;
 
 for (b2=problength-1;b2>=data111(b1,3);--b2){