
R Under development (unstable) (2026-08-27 r90452 ucrt) -- "Unsuffered Consequences"
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> ## This is only for nlmixr
> for (f in c("src/RcppExports.cpp", "inst/include/nlmixr2est_RcppExports.h")) {
+   l <- readLines(f)
+   w <- which(regexpr("^[#]include <RcppArmadillo.h>", l) != -1)
+   if (length(w) == 1) {
+     l <- l[-w]
+     message("Excluding RcppArmadillo from ", f)
+     writeLines(l, f)
+   }
+ }
> 
> unlink("R/nlmixr2_md5.R")
> 
> cpp <- list.files("src", pattern = ".(c|h|cpp|f)$")
> include <- list.files("inst/include")
> Rfiles <- list.files("R/", pattern = ".R")
> md5 <- digest::digest(lapply(c(paste0("src/", cpp),
+                                paste0("inst/include/", include),
+                                paste0("R/", Rfiles)), digest::digest, file = TRUE))
> 
> md5file <- file("R/nlmixr2_md5.R", "wb")
> writeLines(sprintf("nlmixr2.md5 <- \"%s\"\n", md5), md5file)
> close(md5file)
> 
> .in <- suppressWarnings(readLines("src/Makevars.in"))
> 
> .in <- gsub("@ARMA@", file.path(find.package("RcppArmadillo"),"include"), .in)
> .in <- gsub("@BH@", file.path(find.package("BH"),"include"), .in)
> .in <- gsub("@RCPP@", file.path(find.package("Rcpp"),"include"), .in)
> .in <- gsub("@RXP@", file.path(find.package("rxode2"),"include"), .in)
> .in <- gsub("@EG@", file.path(find.package("RcppEigen"),"include"), .in)
> 
> ## COMPATIBILITY PROBE -- remove with the layers it gates (see the follow-up issue).
> ##
> ## rxode2 5.1.6 added setIndCmt() and the event-sensitivity shape save/restore entry
> ## points to the linked function-pointer table.  nlmixr2est uses them when they are
> ## there and falls back to what it did before when they are not, so one source tree
> ## builds against both 5.1.5 and 5.1.6 -- which is what lets the two packages be
> ## submitted to CRAN at the same time.
> ##
> ## Probe the HEADER rather than packageVersion(): the header is what the compile
> ## actually sees, and a source install of an in-between rxode2 can carry either.
> .rxh <- file.path(find.package("rxode2"), "include", "rxode2ptr.h")
> .rxsrc <- if (file.exists(.rxh)) paste(readLines(.rxh, warn = FALSE), collapse = "\n") else ""
> .hasCmtW <- grepl("setIndCmt_t", .rxsrc, fixed = TRUE)
> .hasShape <- grepl("rxode2EventSensShapeSave_t", .rxsrc, fixed = TRUE)
> .compat <- character(0)
> if (.hasCmtW)  .compat <- c(.compat, "-DNLMIXR2EST_HAS_SETINDCMT")
> if (.hasShape) .compat <- c(.compat, "-DNLMIXR2EST_HAS_ESSHAPE")
> message("nlmixr2est: rxode2 API probe -- setIndCmt=", .hasCmtW, " esShape=", .hasShape)
nlmixr2est: rxode2 API probe -- setIndCmt=TRUE esShape=TRUE
> .in <- gsub("@RXCOMPAT@", paste(.compat, collapse = " "), .in)
> 
> 
> if (.Platform$OS.type == "windows") {
+   .makevars <- file("src/Makevars.win", "wb")
+   .i <- "I"
+ } else {
+   .makevars <- file("src/Makevars", "wb")
+   if (any(grepl("Pop!_OS", utils::osVersion, fixed=TRUE)) ||
+         any(grepl("Ubuntu", utils::osVersion, fixed=TRUE))) {
+     .i <- "isystem"
+   } else {
+     .i <- "I"
+   }
+ }
> 
> writeLines(gsub("@ISYSTEM@", .i, .in),
+            .makevars)
> close(.makevars)
> 
> proc.time()
   user  system elapsed 
   0.31    0.26    0.61 
