* installing *source* package ‘rxode2’ ...
** package ‘rxode2’ successfully unpacked and MD5 sums checked
** using staged installation
R Under development (unstable) (2024-04-12 r86412) -- "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)
>
>
>
> if (.Platform$OS.type == "windows" && !file.exists("src/Makevars.win")) {
+ .in <- gsub("@CXX14STD@", "-std=c++1y", .in)
+ file.out <- file("src/Makevars.win", "wb")
+ writeLines(gsub("@ISYSTEM@", "I", .in),
+ file.out)
+ close(file.out)
+ } else {
+ .in <- gsub("@CXX14STD@", "-std=gnu++14", .in)
+ file.out <- file("src/Makevars", "wb")
+ writeLines(gsub("@ISYSTEM@", "isystem", .in),
+ file.out)
+ close(file.out)
+ }
>
> if (file.exists("man/reexports.Rd")) {
+ l <- readLines("man/reexports.Rd")
+ if (!any(regexpr("[\\]value", l) != -1)) {
+ l <- c(l, "\\value{ Inherited from parent routine }")
+ file.out <- file("man/reexports.Rd", "wb")
+ writeLines(l, file.out)
+ close(file.out)
+ }
+ }
>
>
> unlink("R/rxode2_md5.R")
>
> cpp <- list.files("src", pattern = ".(c|h|cpp|f)$")
> include <- list.files("inst/include")
> #Rfiles <- list.files("R/", pattern = ".R")
>
> cmd <- file.path(R.home("bin"), "R")
> args <- c("CMD", "config")
>
> md5 <- digest::digest(c(lapply(c(paste0("src/", cpp),
+ paste0("inst/include/", include)#,
+ #paste0("R/", Rfiles)
+ ), digest::digest, file = TRUE),
+ rxode2parse::rxode2parseMd5(),
+ rxode2random::rxode2randomMd5(),
+ ## 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(file.path(system.file(package="rxode2parse"), "include", "sbuf.c"))
>
> sbuf.c <- file("src/sbuf.c", "wb")
> .w <- which(regexpr(" *extern +SEXP +_goodFuns; *", l) != -1)
> l <- l[-seq(.w, length(l))]
> writeLines(l, sbuf.c)
> close(sbuf.c)
>
> proc.time()
user system elapsed
0.758 0.120 1.151
--------[begin src/Makevars]--------
# -*- mode: makefile-gmake -*-
BH=/data/gannet/ripley/R/test-clang/BH/include
################################################################################
## Package library flags.
PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS)
# Release options
PKG_CFLAGS = -D_isrxode2_
PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"$(BH)"
--------[end src/Makevars]--------
--------[begin R/RxODE_md5.R]--------
rxode2.md5 <- "e494a54d1c17136ec72b60d73c1bfb6f"
--------[end R/RxODE_md5.R]--------
** libs
using C compiler: ‘clang version 18.1.2’
using Fortran compiler: ‘flang-new version 18.1.2’
using C++ compiler: ‘clang version 18.1.2’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rxode2/src'
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/data/gannet/ripley/R/test-clang/BH/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/data/gannet/ripley/R/test-clang/BH/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c boost.cpp -o boost.o
In file included from boost.cpp:12:
In file included from /usr/local/clang/include/boost/math/special_functions/gamma.hpp:17:
In file included from /usr/local/clang/include/boost/math/tools/series.hpp:16:
In file included from /usr/local/clang/include/boost/math/tools/config.hpp:28:
In file included from /usr/local/clang/include/boost/config.hpp:48:
/usr/local/clang/include/boost/config/stdlib/libcpp.hpp:98:11: warning: 'BOOST_NO_AUTO_PTR' macro redefined [-Wmacro-redefined]
98 | # define BOOST_NO_AUTO_PTR
| ^
<command line>:6:9: note: previous definition is here
6 | #define BOOST_NO_AUTO_PTR 1
| ^
1 warning generated.
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/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/clang18/bin/flang-new -fpic -O2 -pedantic -c dlsoda.f -o dlsoda.o
./dlsoda.f:720:2: warning: Compiler directive was ignored
CDIR$ IVDEP
^^^^^^^^^^
./dlsoda.f:844:2: warning: Compiler directive was ignored
CDIR$ IVDEP
^^^^^^^^^^
./dlsoda.f:1015:2: warning: Compiler directive was ignored
CDIR$ IVDEP
^^^^^^^^^^
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/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/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/data/gannet/ripley/R/test-clang/BH/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c etTran.cpp -o etTran.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/data/gannet/ripley/R/test-clang/BH/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c expandGrid.cpp -o expandGrid.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/data/gannet/ripley/R/test-clang/BH/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c expm.cpp -o expm.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/data/gannet/ripley/R/test-clang/BH/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c forder.cpp -o forder.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/flang-new -fpic -O2 -pedantic -c matexp.f -o matexp.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/data/gannet/ripley/R/test-clang/BH/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c nearPD.cpp -o nearPD.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/flang-new -fpic -O2 -pedantic -c opkda2.f -o opkda2.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/data/gannet/ripley/R/test-clang/BH/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c par_solve.cpp -o par_solve.o
In file included from par_solve.cpp:13:
/data/gannet/ripley/R/test-clang/rxode2parse/include/rxode2parseGetTime.h:223:9: warning: unused variable 'curEvid' [-Wunused-variable]
223 | int curEvid = getEvid(ind, ind->idose[*endIdx+1]);
| ^~~~~~~
par_solve.cpp:692:11: warning: lambda capture 'ind' is not used [-Wunused-lambda-capture]
692 | [ind, time](int a, int b){
| ^~~~
par_solve.cpp:749:9: warning: variable 'idid' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
749 | if (!isSameTime(xout, xp)) {
| ^~~~~~~~~~~~~~~~~~~~~
par_solve.cpp:753:9: note: uninitialized use occurs here
753 | if (idid <= 0) {
| ^~~~
par_solve.cpp:749:5: note: remove the 'if' if its condition is always true
749 | if (!isSameTime(xout, xp)) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
par_solve.cpp:746:11: note: initialize the variable 'idid' to silence this warning
746 | int idid, itol=0;
| ^
| = 0
par_solve.cpp:1362:39: warning: variable 'oldI' set but not used [-Wunused-but-set-variable]
1362 | ei=0, wh, cmt, wh100, whI, wh0, oldI,
| ^
par_solve.cpp:1335:7: warning: variable 'maxSS' set but not used [-Wunused-but-set-variable]
1335 | int maxSS = op->maxSS;
| ^
par_solve.cpp:1336:7: warning: variable 'minSS' set but not used [-Wunused-but-set-variable]
1336 | int minSS = op->minSS;
| ^
6 warnings generated.
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/data/gannet/ripley/R/test-clang/BH/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c rxData.cpp -o rxData.o
rxData.cpp:3418:53: warning: variable 'hmax2s' set but not used [-Wunused-but-set-variable]
3418 | hmax1n=0.0, hmax2 = 0.0, hmax2m = 0.0, hmax2mo, hmax2s=0.0,
| ^
rxData.cpp:3935:7: warning: variable 'curEvent' set but not used [-Wunused-but-set-variable]
3935 | int curEvent = 0, curIdx = 0, curSolve=0;
| ^
2 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/data/gannet/ripley/R/test-clang/BH/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c rxInv.cpp -o rxInv.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/data/gannet/ripley/R/test-clang/BH/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c rxOptRep.cpp -o rxOptRep.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/data/gannet/ripley/R/test-clang/BH/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c rxode2_df.cpp -o rxode2_df.o
In file included from rxode2_df.cpp:33:
/data/gannet/ripley/R/test-clang/rxode2parse/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/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/data/gannet/ripley/R/test-clang/BH/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c rxode2parse.cpp -o rxode2parse.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/data/gannet/ripley/R/test-clang/BH/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c rxode2random.cpp -o rxode2random.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/data/gannet/ripley/R/test-clang/BH/include" -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c utilcpp.cpp -o utilcpp.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/rxode2random/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' -isystem /usr/local/clang18/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/clang18/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o rxode2.so RcppExports.o approx.o boost.o box.o call_dvode.o cfode.o cfode_static.o common.o corfailure.o correction.o daxpy.o ddot.o dgefa.o dgesl.o dgpadm.o dlsoda.o dop853.o dscal.o dsphiv.o etTran.o expandGrid.o expm.o fnorm.o forder.o handle_evid.o idamax.o init.o intdy.o lsoda.o matexp.o matexp_HM98.o methodswitch.o nearPD.o omegaChol.o opkda2.o orderswitch.o par_solve.o prja.o rprintf.o rxData.o rxInv.o rxOptRep.o rxode2_df.o rxode2parse.o rxode2random.o sbuf.o scaleh.o solsy.o stoda.o strdup_printf.o strncmp.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 -lFortran_main -lFortranRuntime -lFortranDecimal -lm -fopenmp -lFortran_main -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)