* installing *source* package ‘rxode2’ ...
** package ‘rxode2’ successfully unpacked and MD5 sums checked
** using staged installation
R Under development (unstable) (2024-12-17 r87446) -- "Unsuffered Consequences"
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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$OS.type == "windows") {
+ .makevars <- file("src/Makevars.win", "wb")
+ .i <- "I"
+ } else {
+ .makevars <- file("src/Makevars", "wb")
+ if (any(grepl("Pop!_OS", utils::osVersion, fixed=TRUE))) {
+ .i <- "isystem"
+ } else {
+ .i <- "I"
+ }
+ }
>
> writeLines(gsub("@ISYSTEM@", .i, .in),
+ .makevars)
> close(.makevars)
>
> if (file.exists("man/reexports.Rd")) {
+ l <- readLines("man/reexports.Rd")
+ if (!any(regexpr("[\\]value", l) != -1)) {
+ l <- c(l, "\\value{ Inherited from parent routine }")
+ file.out <- file("man/reexports.Rd", "wb")
+ writeLines(l, file.out)
+ close(file.out)
+ }
+ }
>
>
> unlink("R/rxode2_md5.R")
>
> cpp <- list.files("src", pattern = ".(c|h|cpp|f)$")
> 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
0.761 0.130 2.362
--------[begin src/Makevars]--------
# -*- mode: makefile-gmake -*-
BH=/data/gannet/ripley/R/test-clang/BH/include
RCPP=/data/gannet/ripley/R/test-clang/Rcpp/include
EG=/data/gannet/ripley/R/test-clang/RcppEigen/include
SH=-I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src'
CXX_STD = CXX17
################################################################################
## Package library flags.
PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) -L'/data/gannet/ripley/R/test-clang/RcppParallel/lib/' -Wl,-rpath,'/data/gannet/ripley/R/test-clang/RcppParallel/lib/' -ltbb -ltbbmalloc
# Release options
PKG_CFLAGS = -D_isrxode2_
PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"$(BH)" -I"$(EG)" $(SH) -I"$(RCPP)"
--------[end src/Makevars]--------
--------[begin R/RxODE_md5.R]--------
rxode2.md5 <- "0a237339f256bfcfde66fa049f61dd8e"
--------[end R/RxODE_md5.R]--------
** libs
using C compiler: ‘clang version 19.1.5’
using Fortran compiler: ‘flang-new version 19.1.5’
using C++ compiler: ‘clang version 19.1.5’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rxode2/src'
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:7:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from RcppExports.cpp:7:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
In file included from RcppExports.cpp:7:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
72 | Index replacements = 0;
| ^
In file included from RcppExports.cpp:7:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
246 | int count = 0;
| ^
5 warnings generated.
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c approx.c -o approx.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c boost.cpp -o boost.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c box.c -o box.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c call_dvode.c -o call_dvode.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c cbindThetaOmega.cpp -o cbindThetaOmega.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c cfode.c -o cfode.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c cfode_static.c -o cfode_static.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c checkmate.cpp -o checkmate.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c checkmate_stub.c -o checkmate_stub.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c codegen.c -o codegen.o
codegen.c:344:19: warning: unused variable 'assignOne' [-Wunused-variable]
344 | int assignOne = 0;
| ^~~~~~~~~
1 warning generated.
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c common.c -o common.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c corfailure.c -o corfailure.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c correction.c -o correction.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c cvPost.cpp -o cvPost.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c daxpy.c -o daxpy.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c ddot.c -o ddot.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c dgefa.c -o dgefa.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c dgesl.c -o dgesl.o
/usr/local/clang19/bin/flang-new -fpic -O2 -pedantic -c dgpadm.f -o dgpadm.o
./dgpadm.f:123:7: warning: Reference to the procedure 'dgexx' has an implicit interface that is distinct from another reference: incompatible dummy argument #7: incompatible dummy data object shapes
call DGEXX( 'n','n',m,m,m, 1.0d0,wsp(iused),m,
^
./dgpadm.f:102:7: previous reference to 'dgexx'
call DGEXX( 'n','n',m,m,m,scale2,H,ldh,H,ldh,0.0d0,wsp(ih2),m )
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
./dgpadm.f:138:10: warning: Reference to the procedure 'dgexx' has an implicit interface that is distinct from another reference: incompatible dummy argument #7: incompatible dummy data object shapes
call DGEXX( 'n','n',m,m,m, scale,wsp(iq),m,
^
./dgpadm.f:102:7: previous reference to 'dgexx'
call DGEXX( 'n','n',m,m,m,scale2,H,ldh,H,ldh,0.0d0,wsp(ih2),m )
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
./dgpadm.f:142:10: warning: Reference to the procedure 'dgexx' has an implicit interface that is distinct from another reference: incompatible dummy argument #7: incompatible dummy data object shapes
call DGEXX( 'n','n',m,m,m, scale,wsp(ip),m,
^
./dgpadm.f:102:7: previous reference to 'dgexx'
call DGEXX( 'n','n',m,m,m,scale2,H,ldh,H,ldh,0.0d0,wsp(ih2),m )
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
./dgpadm.f:165:10: warning: Reference to the procedure 'dgexx' has an implicit interface that is distinct from another reference: incompatible dummy argument #7: incompatible dummy data object shapes
call DGEXX( 'n','n',m,m,m, 1.0d0,wsp(iget),m, wsp(iget),m,
^
./dgpadm.f:102:7: previous reference to 'dgexx'
call DGEXX( 'n','n',m,m,m,scale2,H,ldh,H,ldh,0.0d0,wsp(ih2),m )
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/local/clang19/bin/flang-new -fpic -O2 -pedantic -c dlsoda.f -o dlsoda.o
./dlsoda.f:720:7: warning: Unrecognized compiler directive was ignored
CDIR$ IVDEP
^^^^^^
./dlsoda.f:844:7: warning: Unrecognized compiler directive was ignored
CDIR$ IVDEP
^^^^^^
./dlsoda.f:1015:7: warning: Unrecognized compiler directive was ignored
CDIR$ IVDEP
^^^^^^
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c dop853.c -o dop853.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c dscal.c -o dscal.o
/usr/local/clang19/bin/flang-new -fpic -O2 -pedantic -c dsphiv.f -o dsphiv.o
./dsphiv.f:220:12: warning: Reference to the procedure 'daxpy' has an implicit interface that is distinct from another reference: incompatible dummy argument #3: incompatible dummy data object shapes
. call DAXPY(n,-wsp(ih+(j-1)*mh+j-2),wsp(j1v-2*n),1,wsp(j1v),1)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
./dsphiv.f:194:7: previous reference to 'daxpy'
call DAXPY( n, 1.0d0, u,1, wsp(iv),1 )
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
./dsphiv.f:222:10: warning: Reference to the procedure 'daxpy' has an implicit interface that is distinct from another reference: incompatible dummy argument #3: incompatible dummy data object shapes
call DAXPY( n, -hjj, wsp(j1v-n),1, wsp(j1v),1 )
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
./dsphiv.f:194:7: previous reference to 'daxpy'
call DAXPY( n, 1.0d0, u,1, wsp(iv),1 )
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c et.cpp -o et.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c etTran.cpp -o etTran.o
etTran.cpp:784:32: warning: '&&' within '||' [-Wlogical-op-parentheses]
784 | if (hasCmt || covColi >= 0 && as<std::string>(lName[covColi]) != "cmt"){
| ~~ ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
etTran.cpp:784:32: note: place parentheses around the '&&' expression to silence this warning
784 | if (hasCmt || covColi >= 0 && as<std::string>(lName[covColi]) != "cmt"){
| ^
| ( )
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c expandGrid.cpp -o expandGrid.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c expm.cpp -o expm.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c fast_factor.cpp -o fast_factor.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c fnorm.c -o fnorm.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c forder.cpp -o forder.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c genModelVars.c -o genModelVars.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c getOption.c -o getOption.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c handle_evid.c -o handle_evid.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c idamax.c -o idamax.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c init.c -o init.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c intdy.c -o intdy.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c isEt.c -o isEt.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c itostr.c -o itostr.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c lincmt.c -o lincmt.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c lincmtB.cpp -o lincmtB.o
In file included from lincmtB.cpp:64:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:19:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from lincmtB.cpp:64:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:19:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
In file included from lincmtB.cpp:64:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:19:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev.hpp:10:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/fun.hpp:56:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/fun/elt_multiply.hpp:9:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/fun/multiply.hpp:7:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/data/gannet/ripley/R/test-clang/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]
57 | struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> {
| ^
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here?
45 | class ops_partials_edge;
| ^~~~~
| struct
In file included from lincmtB.cpp:64:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:19:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev.hpp:10:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/fun.hpp:201:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:34:
/data/gannet/ripley/R/test-clang/BH/include/boost/units/static_rational.hpp:166:10: warning: extension used [-Wlanguage-extension-token]
166 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
28 | <boost/typeof/incr_registration_group.hpp>
| ^
In file included from lincmtB.cpp:64:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:19:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev.hpp:10:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/fun.hpp:201:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:125:10: warning: extension used [-Wlanguage-extension-token]
125 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
28 | <boost/typeof/incr_registration_group.hpp>
| ^
In file included from lincmtB.cpp:64:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:19:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev.hpp:10:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/fun.hpp:201:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:131:
/data/gannet/ripley/R/test-clang/BH/include/boost/units/dimensionless_type.hpp:49:10: warning: extension used [-Wlanguage-extension-token]
49 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
28 | <boost/typeof/incr_registration_group.hpp>
| ^
In file included from lincmtB.cpp:64:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:19:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev.hpp:10:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/fun.hpp:201:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:39:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/linear_algebra.hpp:20:
/data/gannet/ripley/R/test-clang/BH/include/boost/units/dim.hpp:75:10: warning: extension used [-Wlanguage-extension-token]
75 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
28 | <boost/typeof/incr_registration_group.hpp>
| ^
In file included from lincmtB.cpp:64:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:19:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev.hpp:10:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/fun.hpp:201:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:40:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/unscale.hpp:28:
/data/gannet/ripley/R/test-clang/BH/include/boost/units/scale.hpp:139:10: warning: extension used [-Wlanguage-extension-token]
139 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
28 | <boost/typeof/incr_registration_group.hpp>
| ^
In file included from lincmtB.cpp:64:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:19:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev.hpp:10:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/fun.hpp:201:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20:
/data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:120:10: warning: extension used [-Wlanguage-extension-token]
120 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
28 | <boost/typeof/incr_registration_group.hpp>
| ^
In file included from lincmtB.cpp:64:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:19:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev.hpp:10:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/fun.hpp:201:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:21:
/data/gannet/ripley/R/test-clang/BH/include/boost/units/homogeneous_system.hpp:99:10: warning: extension used [-Wlanguage-extension-token]
99 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
28 | <boost/typeof/incr_registration_group.hpp>
| ^
In file included from lincmtB.cpp:64:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:19:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev.hpp:10:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/fun.hpp:201:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
/data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:495:10: warning: extension used [-Wlanguage-extension-token]
495 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
28 | <boost/typeof/incr_registration_group.hpp>
| ^
In file included from lincmtB.cpp:69:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
72 | Index replacements = 0;
| ^
In file included from lincmtB.cpp:69:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
246 | int count = 0;
| ^
In file included from lincmtB.cpp:108:
./../inst/include/rxode2parseGetTime.h:223:9: warning: unused variable 'curEvid' [-Wunused-variable]
223 | int curEvid = getEvid(ind, ind->idose[*endIdx+1]);
| ^~~~~~~
15 warnings generated.
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c lsoda.c -o lsoda.o
/usr/local/clang19/bin/flang-new -fpic -O2 -pedantic -c matexp.f -o matexp.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c matexp_HM98.c -o matexp_HM98.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c methodswitch.c -o methodswitch.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c nearPD.cpp -o nearPD.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c omegaChol.c -o omegaChol.o
/usr/local/clang19/bin/flang-new -fpic -O2 -pedantic -c opkda2.f -o opkda2.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c orderswitch.c -o orderswitch.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -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]
223 | int curEvid = getEvid(ind, ind->idose[*endIdx+1]);
| ^~~~~~~
par_solve.cpp:647:11: warning: lambda capture 'ind' is not used [-Wunused-lambda-capture]
647 | [ind, time](int a, int b){
| ^~~~
par_solve.cpp:704:9: warning: variable 'idid' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
704 | if (!isSameTime(xout, xp)) {
| ^~~~~~~~~~~~~~~~~~~~~
par_solve.cpp:708:9: note: uninitialized use occurs here
708 | if (idid <= 0) {
| ^~~~
par_solve.cpp:704:5: note: remove the 'if' if its condition is always true
704 | if (!isSameTime(xout, xp)) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
par_solve.cpp:701:11: note: initialize the variable 'idid' to silence this warning
701 | int idid, itol=0;
| ^
| = 0
par_solve.cpp:1317:39: warning: variable 'oldI' set but not used [-Wunused-but-set-variable]
1317 | ei=0, wh, cmt, wh100, whI, wh0, oldI,
| ^
par_solve.cpp:1290:7: warning: variable 'maxSS' set but not used [-Wunused-but-set-variable]
1290 | int maxSS = op->maxSS;
| ^
par_solve.cpp:1291:7: warning: variable 'minSS' set but not used [-Wunused-but-set-variable]
1291 | int minSS = op->minSS;
| ^
6 warnings generated.
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c parseLinCmt.c -o parseLinCmt.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c print_node.c -o print_node.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c prja.c -o prja.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c qs.cpp -o qs.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c rprintf.c -o rprintf.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c rx2api.c -o rx2api.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c rxData.cpp -o rxData.o
rxData.cpp:3583:53: warning: variable 'hmax2s' set but not used [-Wunused-but-set-variable]
3583 | 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]
4148 | int curEvent = 0, curIdx = 0, curSolve=0;
| ^
2 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c rxInv.cpp -o rxInv.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c rxOptRep.cpp -o rxOptRep.o
rxOptRep.cpp:1:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
1 | #define R_NO_REMAP
| ^
<command line>:9:9: note: previous definition is here
9 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c rxStack.cpp -o rxStack.o
rxStack.cpp:59:7: warning: variable 'ncols' set but not used [-Wunused-but-set-variable]
59 | int ncols=3;
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c rxode2_df.cpp -o rxode2_df.o
In file included from rxode2_df.cpp:36:
./../inst/include/rxode2parseGetTime.h:223:9: warning: unused variable 'curEvid' [-Wunused-variable]
223 | int curEvid = getEvid(ind, ind->idose[*endIdx+1]);
| ^~~~~~~
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c rxthreefry.cpp -o rxthreefry.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c sbuf.c -o sbuf.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c scaleh.c -o scaleh.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c seed.cpp -o seed.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c solsy.c -o solsy.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c stoda.c -o stoda.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c strdup_printf.c -o strdup_printf.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c strncmp.c -o strncmp.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c strncmpi.c -o strncmpi.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c tran.c -o tran.o
In file included from tran.c:37:
./tran.g.d_parser.h:3:9: warning: 'printf' macro redefined [-Wmacro-redefined]
3 | #define printf Rprintf
| ^
/usr/include/bits/stdio2.h:89:11: note: previous definition is here
89 | # define printf(...) \
| ^
In file included from tran.c:155:
./parseAssignStr.h:129:13: warning: unused variable 'buf' [-Wunused-variable]
129 | char *buf = tb.str.line[tb.id];
| ^~~
In file included from tran.c:156:
./parseLevels.h:94:11: warning: unused variable 'n' [-Wunused-variable]
94 | int n = get_str_assign_int(tb.id, v);
| ^
3 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c udf.cpp -o udf.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c utilc.c -o utilc.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -I'/data/gannet/ripley/R/test-clang/StanHeaders/include/src' -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c utilcpp.cpp -o utilcpp.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/sitmo/include' -I'/data/gannet/ripley/R/test-clang/lotri/include' -I'/data/gannet/ripley/R/test-clang/PreciseSums/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/dparser/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -D_isrxode2_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c vmnorm.c -o vmnorm.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -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/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortranRuntime -lFortranDecimal -lm -fopenmp -L/data/gannet/ripley/R/test-clang/RcppParallel/lib/ -Wl,-rpath,/data/gannet/ripley/R/test-clang/RcppParallel/lib/ -ltbb -ltbbmalloc -lFortranRuntime -lFortranDecimal -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rxode2/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rxode2/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rxode2/src'
installing via 'install.libs.R' to /data/gannet/ripley/R/packages/tests-clang/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)