* installing *source* package ‘rxode2’ ... ** package ‘rxode2’ successfully unpacked and MD5 sums checked ** using staged installation R Under development (unstable) (2024-04-24 r86484) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > ## This is only for rxode2 > for (f in c("inst/include/rxode2_RcppExports.h", "src/RcppExports.cpp")) { + l <- readLines(f) + w <- which(regexpr("^[#]include ", 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 ", + 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 0.776 0.108 1.482 --------[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 18.1.4’ using Fortran compiler: ‘flang-new version 18.1.4’ using C++ compiler: ‘clang version 18.1.4’ 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 | ^ :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)