* installing *source* package ‘rxode2’ ...
** package ‘rxode2’ successfully unpacked and MD5 sums checked
** using staged installation
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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> ## This is only for rxode2
> for (f in c("inst/include/rxode2_RcppExports.h", "src/RcppExports.cpp")) {
+ l <- readLines(f)
+ w <- which(regexpr("^[#]include <RcppArmadillo.h>", l) != -1)
+ if (length(w) > 0) {
+ l <- l[-w]
+ }
+ w <- which(regexpr("^[#]define R_STRICT_HEADERS", l) != -1)
+ if (length(w) > 0) {
+ l <- l[-w]
+ }
+ l <- c("#define R_STRICT_HEADERS",
+ "#include <RcppArmadillo.h>",
+ l)
+ file.out <- file(f, "wb")
+ writeLines(l, file.out)
+ close(file.out)
+ }
>
> l <- readLines("R/RcppExports.R")
> w <- which(regexpr("# Register entry points", l, fixed=TRUE) != -1)
> if (length(w) >= 1) {
+ w <- w[1]
+ l <- l[seq(1, w-1)]
+ RcppExports.R <- file("R/RcppExports.R", "wb")
+ writeLines(l, RcppExports.R)
+ close(RcppExports.R)
+ }
>
> .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("@EG@", file.path(find.package("RcppEigen"),"include"), .in)
>
> .in <- gsub("@SL@", paste(capture.output(StanHeaders:::LdFlags()), capture.output(RcppParallel:::RcppParallelLibs())), #nolint
+ .in)
>
>
> .badStan <- ""
> .in <- gsub("@SH@", gsub("-I", "-@ISYSTEM@",
+ paste(capture.output(StanHeaders:::CxxFlags()), # nolint
+ capture.output(RcppParallel:::CxxFlags()), # nolint
+ paste0("-@ISYSTEM@'", system.file('include', 'src', package = 'StanHeaders', mustWork = TRUE), "'"),
+ .badStan)),
+ .in)
>
>
>
>
> if (.Platform$OS.type == "windows" && !file.exists("src/Makevars.win")) {
+ .in <- gsub("@CXX14STD@", "-std=c++1y", .in)
+ file.out <- file("src/Makevars.win", "wb")
+ writeLines(gsub("@ISYSTEM@", "I", .in),
+ file.out)
+ close(file.out)
+ } else {
+ .in <- gsub("@CXX14STD@", "-std=gnu++14", .in)
+ file.out <- file("src/Makevars", "wb")
+ writeLines(gsub("@ISYSTEM@", "isystem", .in),
+ file.out)
+ close(file.out)
+ }
>
> if (file.exists("man/reexports.Rd")) {
+ l <- readLines("man/reexports.Rd")
+ if (!any(regexpr("[\\]value", l) != -1)) {
+ l <- c(l, "\\value{ Inherited from parent routine }")
+ file.out <- file("man/reexports.Rd", "wb")
+ writeLines(l, file.out)
+ close(file.out)
+ }
+ }
>
>
> unlink("R/rxode2_md5.R")
>
> cpp <- list.files("src", pattern = ".(c|h|cpp|f)$")
> include <- list.files("inst/include")
> #Rfiles <- list.files("R/", pattern = ".R")
>
> cmd <- file.path(R.home("bin"), "R")
> args <- c("CMD", "config")
>
> md5 <- digest::digest(c(lapply(c(paste0("src/", cpp),
+ paste0("inst/include/", include)#,
+ #paste0("R/", Rfiles)
+ ), digest::digest, file = TRUE),
+ ## vapply(c("BLAS_LIBS", "CC", "CFLAGS", "CPICFLAGS",
+ ## "CXX", "CXXFLAGS", "CXXPICFLAGS",
+ ## "CXX11", "CXX11STD", "CXX11FLAGS", "CXX11PICFLAGS",
+ ## "CXX14", "CXX14STD", "CXX14FLAGS", "CXX14PICFLAGS",
+ ## "CXX17", "CXX17STD", "CXX17FLAGS", "CXX17PICFLAGS",
+ ## "CXX20", "CXX20STD", "CXX20FLAGS", "CXX20PICFLAGS",
+ ## "FC", "FFLAGS", "FCFLAGS", "FPICFLAGS"),
+ ## function(cfg) {
+ ## rawToChar(sys::exec_internal(cmd, c(args, cfg))$stdout)
+ ## }, character(1)
+ ## ),
+ ""
+ ))
> unlink("R/rxode2_md5.R")
> md5file <- file("R/rxode2_md5.R", "wb")
> writeLines(sprintf("rxode2.md5 <- \"%s\"\n", md5), md5file)
> close(md5file)
>
> l <- readLines("DESCRIPTION")
> w <- which(regexpr("Version[:] *(.*)$", l) != -1)
> v <- gsub("Version[:] *(.*)$", "\\1", l[w])
>
> unlink("inst/include/rxode2parseVer.h")
> ode.h <- file("inst/include/rxode2parseVer.h", "wb")
> writeLines(c(sprintf("#define __VER_md5__ \"%s\"", md5),
+ "#define __VER_repo__ \"https://github.com/nlmixr2/rxode2\"",
+ sprintf("#define __VER_ver__ \"%s\"", v)),
+ ode.h)
> close(ode.h)
>
> unlink("src/sbuf.c")
> l <- readLines("inst/include/sbuf.c")
> sbuf.c <- file("src/sbuf.c", "wb")
> writeLines(l, sbuf.c)
> close(sbuf.c)
>
>
> unlink("src/codegen2.h")
> l <- readLines("inst/include/rxode2_model_shared.c")
>
> l <- l[l != ""]
> l <- gsub(" *= *NULL;", "=NULL;", l)
>
> def <- l
> w <- which(regexpr("double _prod", def) != -1) - 1
> def <- def[1:w]
> def <- gsub("=NULL", "", def)
> def <- gsub("[^ ]* *[*]?([^;]*);", "\\1", def)
>
> def <- unique(c(def, c("_sum", "_udf", "_sign", "_prod", "_max", "_min", "_transit4P", "_transit3P", "_assignFuns0", "_assignFuns", "_getRxSolve_", "_solveData", "_rxord", "__assignFuns2")))
>
> w0 <- which(grepl("double +_prod", l))[1]
> r <- 1:(w0 - 1)
> l0 <- l[r]
> l <- l[-r]
>
>
> w1 <- which(regexpr("dynamic start", l) != -1)
> l1 <- l[1:w1]
>
>
>
> w2 <- which(regexpr("dynamic stop", l) != -1)
> l2 <- l[seq(w2, length(l))]
>
> w3 <- which(regexpr("assign start", l2) != -1)
>
> l3 <- l2[seq(w3, length(l2))]
> l2 <- l2[1:w3]
>
> w4 <- which(regexpr("assign stop", l3) != -1)
> l3 <- l3[seq(w4, length(l3))]
>
> dfP <- l[seq(w1+1, w2-1)]
>
> dfP <- dfP[regexpr("^ *$", dfP)==-1]
> df <- setNames(do.call("rbind",lapply(seq_along(dfP),
+ function(i) {
+ .r <- sub("^ *", "", dfP[[i]])
+ .r <- sub("^([^ ]*) *= *[(]", "\\1,", .r)
+ .r <- sub("^([^ ]*) *[)] *R_GetCCallable *[(] *\"", "\\1,", .r, perl=TRUE)
+ .r <- sub("^([^ ]*) *\" *, *\"", "\\1,", .r, perl=TRUE)
+ .r <- sub("^([^ ]*)\" *[)] *; *", "\\1",.r, perl=TRUE)
+ data.frame(t(strsplit(.r, ",")[[1]]),stringsAsFactors = FALSE)
+ })), c("fun", "type", "package", "packageFun"))
>
> df$rxFun <- df$fun
> df$argMax <- df$argMin <- NA_integer_
> df$threadSafe <- 1L
> df <- df[,c("rxFun", "fun", "type", "package", "packageFun", "argMin", "argMax", "threadSafe")]
> df$rxFun <- gsub("_llik", "llik", df$rxFun)
>
> def <- def[!(def %in% df$rxFun)]
> def <- def[!(def %in% df$fun)]
>
> .parseEnv <- new.env(parent=emptyenv())
> source("R/parseFuns.R")
>
> df$argMin <- vapply(df$rxFun, function(f) {
+ .n <- .parseEnv$.parseNum[f]
+ if (is.na(.n)) return(NA_integer_)
+ .n <-setNames(.n, NULL)
+ as.integer(.n)
+ }, integer(1), USE.NAMES=TRUE)
>
> df$argMax <- df$argMin
>
> dfStr <- deparse(df)
> dfStr[1] <- paste(".parseEnv$.rxode2parseDf <- ", dfStr[1])
>
> dfIni.R <- file("R/dfIni.R", "wb")
> writeLines(dfStr,
+ dfIni.R)
> close(dfIni.R)
>
> ## deparse1 came from R 4.0, use deparse2
> deparse2 <- function(expr, collapse = " ", width.cutoff = 500L, ...) {
+ paste(deparse(expr, width.cutoff, ...), collapse = collapse)
+ }
>
> final <- c("#include <time.h>",
+ "#include <stdlib.h>",
+ "unsigned long int __timeId=0;",
+ "void writeHeader(const char *md5, const char *extra) {",
+ paste0("sAppend(&sbOut, \"#define ", def, " _rx%s%s%ld\\n\", extra, md5, __timeId++);"),
+ "}",
+ "void writeBody0(void) {",
+ paste0("sAppendN(&sbOut, ", vapply(paste0(l0, "\n"), deparse2, character(1)), ", ", nchar(l0) + 1, ");"),
+ "}",
+ "void writeBody1(void) {",
+ paste0("sAppendN(&sbOut, ", vapply(paste0(l1, "\n"), deparse2, character(1)), ", ", nchar(l1) + 1, ");"),
+ "}",
+ "void writeBody2(void) {",
+ paste0("sAppendN(&sbOut, ", vapply(paste0(l2, "\n"), deparse2, character(1)), ", ", nchar(l2) + 1, ");"),
+ "}",
+ "void writeBody3(void) {",
+ paste0("sAppendN(&sbOut, ", vapply(paste0(l3, "\n"), deparse2, character(1)), ", ", nchar(l3) + 1, ");"),
+ "}",
+ "void writeFooter(void) {",
+ paste0("sAppendN(&sbOut, \"#undef ", def, "\\n\", ", nchar(def) + 8, ");"),
+ "}"
+ )
>
> codegen2.h <- file("src/codegen2.h", "wb")
> writeLines(final,
+ codegen2.h)
> close(codegen2.h)
>
> proc.time()
user system elapsed
0.291 0.078 0.368
--------[begin src/Makevars]--------
# -*- mode: makefile-gmake -*-
BH=/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include
RCPP=/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include
EG=/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include
SH=-isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src'
CXX_STD = CXX17
################################################################################
## Package library flags.
PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) -L'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/lib/' -Wl,-rpath,'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/lib/' -ltbb -ltbbmalloc -L/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/lib -ltbb -ltbbmalloc
# Release options
PKG_CFLAGS = -D_isrxode2_
PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"$(BH)" -isystem"$(EG)" $(SH) -isystem"$(RCPP)"
--------[end src/Makevars]--------
--------[begin R/RxODE_md5.R]--------
rxode2.md5 <- "81d3f05c9cb380efff615aa6e88cf4c4"
--------[end R/RxODE_md5.R]--------
** libs
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using C++17
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c approx.c -o approx.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c boost.cpp -o boost.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c box.c -o box.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c call_dvode.c -o call_dvode.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c cbindThetaOmega.cpp -o cbindThetaOmega.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c cfode.c -o cfode.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c cfode_static.c -o cfode_static.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c checkmate.cpp -o checkmate.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c checkmate_stub.c -o checkmate_stub.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c codegen.c -o codegen.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c common.c -o common.o
codegen.c:344:19: warning: unused variable 'assignOne' [-Wunused-variable]
int assignOne = 0;
^
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c corfailure.c -o corfailure.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c correction.c -o correction.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c cvPost.cpp -o cvPost.o
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c daxpy.c -o daxpy.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c ddot.c -o ddot.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c dgefa.c -o dgefa.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c dgesl.c -o dgesl.o
/opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c dgpadm.f -o dgpadm.o
/opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c dlsoda.f -o dlsoda.o
dlsoda.f:2874:72:
2874 | IF (IHIT) T = TCRIT
| ^
Warning: ‘tcrit’ may be used uninitialized [-Wmaybe-uninitialized]
dlsoda.f:2413:14:
2413 | 1 TCRIT, TDIST, TNEXT, TOL, TOLSF, TP, SIZE, SUM, W0
| ^
note: ‘tcrit’ was declared here
dlsoda.f:2874:10:
2874 | IF (IHIT) T = TCRIT
| ^
Warning: ‘ihit’ may be used uninitialized [-Wmaybe-uninitialized]
dlsoda.f:2415:18:
2415 | LOGICAL IHIT
| ^
note: ‘ihit’ was declared here
dlsoda.f:2615:29:
2615 | IF (H0 .NE. 0.0D0 .AND. (T + H0 - TCRIT)*H0 .GT. 0.0D0)
| ^
Warning: ‘h0’ may be used uninitialized [-Wmaybe-uninitialized]
dlsoda.f:2412:48:
2412 | DOUBLE PRECISION ATOLI, AYI, BIG, EWTI, H0, HMAX, HMX, RH, RTOLI,
| ^
note: ‘h0’ was declared here
dlsoda.f:2536:72:
2536 | IF (JT .GE. 4) LENWM = (2*ML + MU + 1)*N + 2
| ^
Warning: ‘mu’ may be used uninitialized [-Wmaybe-uninitialized]
dlsoda.f:2407:42:
2407 | 1 LENIW, LENRW, LENWM, ML, MORD, MU, MXHNL0, MXSTP0
| ^
note: ‘mu’ was declared here
dlsoda.f:2536:72:
2536 | IF (JT .GE. 4) LENWM = (2*ML + MU + 1)*N + 2
| ^
Warning: ‘ml’ may be used uninitialized [-Wmaybe-uninitialized]
dlsoda.f:2407:32:
2407 | 1 LENIW, LENRW, LENWM, ML, MORD, MU, MXHNL0, MXSTP0
| ^
note: ‘ml’ was declared here
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c dop853.c -o dop853.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c dscal.c -o dscal.o
/opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c dsphiv.f -o dsphiv.o
dsphiv.f:270:72:
270 | wsp(iphih+mbrkdwn+1) = hj1j*wsp(iphih+2*mx+mbrkdwn-1)
| ^
Warning: ‘hj1j’ may be used uninitialized [-Wmaybe-uninitialized]
dsphiv.f:125:35:
125 | . avnorm, hj1j, hjj, SQR1
| ^
note: ‘hj1j’ was declared here
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c et.cpp -o et.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c etTran.cpp -o etTran.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c expandGrid.cpp -o expandGrid.o
etTran.cpp:784:32: warning: '&&' within '||' [-Wlogical-op-parentheses]
if (hasCmt || covColi >= 0 && as<std::string>(lName[covColi]) != "cmt"){
~~ ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
etTran.cpp:784:32: note: place parentheses around the '&&' expression to silence this warning
if (hasCmt || covColi >= 0 && as<std::string>(lName[covColi]) != "cmt"){
^
( )
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c expm.cpp -o expm.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c fast_factor.cpp -o fast_factor.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c fnorm.c -o fnorm.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c forder.cpp -o forder.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c genModelVars.c -o genModelVars.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c getOption.c -o getOption.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c handle_evid.c -o handle_evid.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c idamax.c -o idamax.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c intdy.c -o intdy.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c isEt.c -o isEt.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c itostr.c -o itostr.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c lincmt.c -o lincmt.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c lincmtB.cpp -o lincmtB.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c lsoda.c -o lsoda.o
/opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c matexp.f -o matexp.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c matexp_HM98.c -o matexp_HM98.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c methodswitch.c -o methodswitch.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c nearPD.cpp -o nearPD.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c omegaChol.c -o omegaChol.o
In file included from lincmtB.cpp:64:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math.hpp:19:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/rev.hpp:10:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/rev/fun.hpp:56:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/rev/fun/elt_multiply.hpp:9:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/rev/fun/multiply.hpp:7:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> {
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here?
class ops_partials_edge;
^~~~~
struct
/opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c opkda2.f -o opkda2.o
opkda2.f:650:28:
650 | INTEGER FUNCTION IXSAV (IPAR, IVALUE, ISET)
| ^
Warning: ‘__result_ixsav’ may be used uninitialized [-Wmaybe-uninitialized]
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c orderswitch.c -o orderswitch.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c par_solve.cpp -o par_solve.o
In file included from par_solve.cpp:15:
./../inst/include/rxode2parseGetTime.h:223:9: warning: unused variable 'curEvid' [-Wunused-variable]
int curEvid = getEvid(ind, ind->idose[*endIdx+1]);
^
par_solve.cpp:647:11: warning: lambda capture 'ind' is not used [-Wunused-lambda-capture]
[ind, time](int a, int b){
^~~~
par_solve.cpp:704:9: warning: variable 'idid' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if (!isSameTime(xout, xp)) {
^~~~~~~~~~~~~~~~~~~~~
par_solve.cpp:708:9: note: uninitialized use occurs here
if (idid <= 0) {
^~~~
par_solve.cpp:704:5: note: remove the 'if' if its condition is always true
if (!isSameTime(xout, xp)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~
par_solve.cpp:701:11: note: initialize the variable 'idid' to silence this warning
int idid, itol=0;
^
= 0
par_solve.cpp:1317:39: warning: variable 'oldI' set but not used [-Wunused-but-set-variable]
ei=0, wh, cmt, wh100, whI, wh0, oldI,
^
par_solve.cpp:1290:7: warning: variable 'maxSS' set but not used [-Wunused-but-set-variable]
int maxSS = op->maxSS;
^
par_solve.cpp:1291:7: warning: variable 'minSS' set but not used [-Wunused-but-set-variable]
int minSS = op->minSS;
^
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c parseLinCmt.c -o parseLinCmt.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c print_node.c -o print_node.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c prja.c -o prja.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c qs.cpp -o qs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c rprintf.c -o rprintf.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c rx2api.c -o rx2api.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c rxData.cpp -o rxData.o
6 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c rxInv.cpp -o rxInv.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c rxOptRep.cpp -o rxOptRep.o
In file included from lincmtB.cpp:108:
./../inst/include/rxode2parseGetTime.h:223:9: warning: unused variable 'curEvid' [-Wunused-variable]
int curEvid = getEvid(ind, ind->idose[*endIdx+1]);
^
rxData.cpp:3583:53: warning: variable 'hmax2s' set but not used [-Wunused-but-set-variable]
hmax1n=0.0, hmax2 = 0.0, hmax2m = 0.0, hmax2mo, hmax2s=0.0,
^
rxData.cpp:4148:7: warning: variable 'curEvent' set but not used [-Wunused-but-set-variable]
int curEvent = 0, curIdx = 0, curSolve=0;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c rxStack.cpp -o rxStack.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c rxode2_df.cpp -o rxode2_df.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c rxthreefry.cpp -o rxthreefry.o
rxStack.cpp:59:7: warning: variable 'ncols' set but not used [-Wunused-but-set-variable]
int ncols=3;
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c sbuf.c -o sbuf.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c scaleh.c -o scaleh.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c seed.cpp -o seed.o
In file included from rxode2_df.cpp:36:
./../inst/include/rxode2parseGetTime.h:223:9: warning: unused variable 'curEvid' [-Wunused-variable]
int curEvid = getEvid(ind, ind->idose[*endIdx+1]);
^
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c solsy.c -o solsy.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c stoda.c -o stoda.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c strdup_printf.c -o strdup_printf.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c strncmp.c -o strncmp.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c strncmpi.c -o strncmpi.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c tran.c -o tran.o
In file included from tran.c:155:
./parseAssignStr.h:129:13: warning: unused variable 'buf' [-Wunused-variable]
char *buf = tb.str.line[tb.id];
^
In file included from tran.c:156:
./parseLevels.h:94:11: warning: unused variable 'n' [-Wunused-variable]
int n = get_str_assign_int(tb.id, v);
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c udf.cpp -o udf.o
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c utilc.c -o utilc.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include" -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include" -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -isystem'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include/src' -isystem"/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include" -fPIC -falign-functions=64 -Wall -g -O2 -c utilcpp.cpp -o utilcpp.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/sitmo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/lotri/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/PreciseSums/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/StanHeaders/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/dparser/include' -I/opt/R/x86_64/include -D_isrxode2_ -fPIC -falign-functions=64 -Wall -g -O2 -c vmnorm.c -o vmnorm.o
2 warnings generated.
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o rxode2.so RcppExports.o approx.o boost.o box.o call_dvode.o cbindThetaOmega.o cfode.o cfode_static.o checkmate.o checkmate_stub.o codegen.o common.o corfailure.o correction.o cvPost.o daxpy.o ddot.o dgefa.o dgesl.o dgpadm.o dlsoda.o dop853.o dscal.o dsphiv.o et.o etTran.o expandGrid.o expm.o fast_factor.o fnorm.o forder.o genModelVars.o getOption.o handle_evid.o idamax.o init.o intdy.o isEt.o itostr.o lincmt.o lincmtB.o lsoda.o matexp.o matexp_HM98.o methodswitch.o nearPD.o omegaChol.o opkda2.o orderswitch.o par_solve.o parseLinCmt.o print_node.o prja.o qs.o rprintf.o rx2api.o rxData.o rxInv.o rxOptRep.o rxStack.o rxode2_df.o rxthreefry.o sbuf.o scaleh.o seed.o solsy.o stoda.o strdup_printf.o strncmp.o strncmpi.o tran.o udf.o utilc.o utilcpp.o vmnorm.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -L/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/lib/ -Wl,-rpath,/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/lib/ -ltbb -ltbbmalloc -L/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppParallel/lib -ltbb -ltbbmalloc -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing via 'install.libs.R' to /Volumes/Builds/packages/big-sur-x86_64/results/4.4/rxode2.Rcheck/00LOCK-rxode2/00new/rxode2
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rxode2)