Merge branch 'LTO_again'

stan-dev · Jan 16, 2024 · 4c39379 · 4c39379
2 parents 5b0c0df + b443d2e
commit 4c39379
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: rstanarm
 Type: Package
 Title: Bayesian Applied Regression Modeling via Stan
-Version: 2.26.1
-Date: 2023-09-13
+Version: 2.32l1
+Date: 2024-01-15
 Encoding: UTF-8
 Authors@R: c(person("Jonah", "Gabry", email = "[email protected]", role = "aut"),
              person("Imad", "Ali", role = "ctb"),
@@ -42,7 +42,7 @@ Imports:
     Matrix (>= 1.2-13),
     nlme (>= 3.1-124),
     posterior, 
-    rstan (>= 2.26.1),
+    rstan (>= 2.32.0),
     rstantools (>= 2.1.0),
     shinystan (>= 2.3.0),
     stats,
@@ -64,8 +64,9 @@ Suggests:
     StanHeaders (>= 2.21.0),
     testthat (>= 1.0.2),
     gamm4,
-    shiny
-LinkingTo: StanHeaders (>= 2.21.0), rstan (>= 2.21.1), BH (>= 1.72.0-2), Rcpp (>=
+    shiny,
+    V8
+LinkingTo: StanHeaders (>= 2.32.0), rstan (>= 2.32.0), BH (>= 1.72.0-2), Rcpp (>=
     0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1)
 SystemRequirements: GNU make, pandoc (>= 1.12.3), pandoc-citeproc
 VignetteBuilder: knitr

diff --git a/R/doc-datasets.R b/R/doc-datasets.R
@@ -86,21 +86,21 @@
 #' 
 #' 304 obs. of 8 variables (\code{pbcLong}) and 40 obs. of 7 variables (\code{pbcSurv})
 #' \itemize{
-#' \item \code{age} {in years}
-#' \item \code{albumin} {serum albumin (g/dl)}
-#' \item \code{logBili} {logarithm of serum bilirubin}
-#' \item \code{death} {indicator of death at endpoint} 
-#' \item \code{futimeYears} {time (in years) between baseline and  
-#'     the earliest of death, transplantion or censoring}
-#' \item \code{id} {numeric ID unique to each individual}
-#' \item \code{platelet} {platelet count}
-#' \item \code{sex} {gender (m = male, f = female)}
-#' \item \code{status} {status at endpoint (0 = censored, 
-#'     1 = transplant, 2 = dead)}
-#' \item \code{trt} {binary treatment code (0 = placebo, 1 = 
-#'     D-penicillamine)}
-#' \item \code{year} {time (in years) of the longitudinal measurements,
-#'     taken as time since baseline)}
+#' \item \code{age} in years
+#' \item \code{albumin} serum albumin (g/dl)
+#' \item \code{logBili} logarithm of serum bilirubin
+#' \item \code{death} indicator of death at endpoint
+#' \item \code{futimeYears} time (in years) between baseline and  
+#'     the earliest of death, transplantion or censoring
+#' \item \code{id} numeric ID unique to each individual
+#' \item \code{platelet} platelet count
+#' \item \code{sex} gender (m = male, f = female)
+#' \item \code{status} status at endpoint (0 = censored, 
+#'     1 = transplant, 2 = dead)
+#' \item \code{trt} binary treatment code (0 = placebo, 1 = 
+#'     D-penicillamine)
+#' \item \code{year} time (in years) of the longitudinal measurements,
+#'     taken as time since baseline)
 #' }
 #' }
 #' 

diff --git a/src/Makevars b/src/Makevars
@@ -2,7 +2,7 @@ STANHEADERS_SRC = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "message()" -e
 
 STANC_FLAGS = -DUSE_STANC3
 PKG_CPPFLAGS = -I"../inst/include" -I"$(STANHEADERS_SRC)" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error $(STANC_FLAGS) -D_HAS_AUTO_PTR_ETC=0
-PKG_CXXFLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::CxxFlags()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::CxxFlags()")
+PKG_CXXFLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::CxxFlags()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::CxxFlags()") $(LTO)
 PKG_LIBS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::RcppParallelLibs()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::LdFlags()")
 SHLIB_LDFLAGS = $(SHLIB_CXXLDFLAGS)
 SHLIB_LD = $(SHLIB_CXXLD)