Update deprecated syntax and fix vignettes #1055
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The Stan code used in the examples & vignettes (and some of the demonstrative c++) has since been deprecated or removed. Additionally, the vignettes were failing to build due to some configuration/compilation issues.
The following changes have been made in this PR:
rstan
examples and vignettes updated to remove any deprecated syntaxStanHeaders
was not compilingsundials/sundials_context.c
under unix, leading to ODE linking errors in the vignetteStanHeaders::stanFunction()
was not using the package's CXXFLAGS, leading to compilation errors due to the missing-D_REENTRANT
under unix when building the vignetterstan
external c++ vignette was usingstan::math::precomp_v_vari()
which has since been removed