* installing *source* package ‘rxode2’ ...
** package ‘rxode2’ successfully unpacked and MD5 sums checked
** using staged installation
R Under development (unstable) (2024-04-11 r86406) -- "Unsuffered Consequences"
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Platform: x86_64-pc-linux-gnu
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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
0.767 0.125 1.517
--------[begin src/Makevars]--------
# -*- mode: makefile-gmake -*-
BH=/data/gannet/ripley/R/test-dev/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: ‘gcc-13 (GCC) 13.2.0’
using Fortran compiler: ‘GNU Fortran (GCC) 13.2.0’
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/rxode2/src'
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/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-dev/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c approx.c -o approx.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/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-dev/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c boost.cpp -o boost.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c box.c -o box.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c call_dvode.c -o call_dvode.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cfode.c -o cfode.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cfode_static.c -o cfode_static.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c common.c -o common.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c corfailure.c -o corfailure.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c correction.c -o correction.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c daxpy.c -o daxpy.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c ddot.c -o ddot.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c dgefa.c -o dgefa.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c dgesl.c -o dgesl.o
gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -c dgpadm.f -o dgpadm.o
gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -c dlsoda.f -o dlsoda.o
dlsoda.f:2536:72:
2536 | IF (JT .GE. 4) LENWM = (2*ML + MU + 1)*N + 2
| ^
Warning: 'ml' may be used uninitialized [-Wmaybe-uninitialized]
dlsoda.f:2407:32:
2407 | 1 LENIW, LENRW, LENWM, ML, MORD, MU, MXHNL0, MXSTP0
| ^
note: 'ml' was declared here
dlsoda.f:2536:72:
2536 | IF (JT .GE. 4) LENWM = (2*ML + MU + 1)*N + 2
| ^
Warning: 'mu' may be used uninitialized [-Wmaybe-uninitialized]
dlsoda.f:2407:42:
2407 | 1 LENIW, LENRW, LENWM, ML, MORD, MU, MXHNL0, MXSTP0
| ^
note: 'mu' was declared here
dlsoda.f:2615:29:
2615 | IF (H0 .NE. 0.0D0 .AND. (T + H0 - TCRIT)*H0 .GT. 0.0D0)
| ^
Warning: 'h0' may be used uninitialized [-Wmaybe-uninitialized]
dlsoda.f:2412:48:
2412 | DOUBLE PRECISION ATOLI, AYI, BIG, EWTI, H0, HMAX, HMX, RH, RTOLI,
| ^
note: 'h0' was declared here
dlsoda.f:2851:72:
2851 | IHIT = ABS(TN - TCRIT) .LE. 100.0D0*UROUND*HMX
| ^
Warning: 'tcrit' may be used uninitialized [-Wmaybe-uninitialized]
dlsoda.f:2413:14:
2413 | 1 TCRIT, TDIST, TNEXT, TOL, TOLSF, TP, SIZE, SUM, W0
| ^
note: 'tcrit' was declared here
dlsoda.f:2874:10:
2874 | IF (IHIT) T = TCRIT
| ^
Warning: 'ihit' may be used uninitialized [-Wmaybe-uninitialized]
dlsoda.f:2415:18:
2415 | LOGICAL IHIT
| ^
note: 'ihit' was declared here
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c dop853.c -o dop853.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c dscal.c -o dscal.o
gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -c dsphiv.f -o dsphiv.o
dsphiv.f:270:72:
270 | wsp(iphih+mbrkdwn+1) = hj1j*wsp(iphih+2*mx+mbrkdwn-1)
| ^
Warning: 'hj1j' may be used uninitialized [-Wmaybe-uninitialized]
dsphiv.f:125:35:
125 | . avnorm, hj1j, hjj, SQR1
| ^
note: 'hj1j' was declared here
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/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-dev/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c etTran.cpp -o etTran.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/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-dev/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c expandGrid.cpp -o expandGrid.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/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-dev/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c expm.cpp -o expm.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c fnorm.c -o fnorm.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/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-dev/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c forder.cpp -o forder.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c handle_evid.c -o handle_evid.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c idamax.c -o idamax.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c init.c -o init.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c intdy.c -o intdy.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c lsoda.c -o lsoda.o
gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -c matexp.f -o matexp.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c matexp_HM98.c -o matexp_HM98.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c methodswitch.c -o methodswitch.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/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-dev/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c nearPD.cpp -o nearPD.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c omegaChol.c -o omegaChol.o
gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -c opkda2.f -o opkda2.o
opkda2.f:650:28:
650 | INTEGER FUNCTION IXSAV (IPAR, IVALUE, ISET)
| ^
Warning: '__result_ixsav' may be used uninitialized [-Wmaybe-uninitialized]
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c orderswitch.c -o orderswitch.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/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-dev/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c par_solve.cpp -o par_solve.o
In file included from par_solve.cpp:13:
/data/gannet/ripley/R/test-dev/rxode2parse/include/rxode2parseGetTime.h: In function 'int handleInfusionStartRm(int*, int*, double*, int*, rx_solve*, rx_solving_options*, rx_solving_options_ind*)':
/data/gannet/ripley/R/test-dev/rxode2parse/include/rxode2parseGetTime.h:223:9: warning: unused variable 'curEvid' [-Wunused-variable]
223 | int curEvid = getEvid(ind, ind->idose[*endIdx+1]);
| ^~~~~~~
par_solve.cpp: In function 'void handleSS(int*, int*, double*, double*, double*, double, double, int, int*, int, int*, rx_solving_options*, rx_solving_options_ind*, t_update_inis, void*)':
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,
| ^~~~
/data/gannet/ripley/R/test-dev/rxode2parse/include/rxode2parseGetTime.h: In function 'double handleInfusionItem(int, rx_solve*, rx_solving_options*, rx_solving_options_ind*)':
/data/gannet/ripley/R/test-dev/rxode2parse/include/rxode2parseGetTime.h:314:5: warning: 'infBidx' may be used uninitialized [-Wmaybe-uninitialized]
314 | if (infBidx == -1) return 0.0;
| ^~
/data/gannet/ripley/R/test-dev/rxode2parse/include/rxode2parseGetTime.h:312:9: note: 'infBidx' was declared here
312 | int infBidx;
| ^~~~~~~
par_solve.cpp: In function 'void solveWith1Pt(int*, int*, double*, double*, double*, double, double, int, int*, int, int*, rx_solving_options*, rx_solving_options_ind*, t_update_inis, void*)':
par_solve.cpp:753:5: warning: 'idid' may be used uninitialized [-Wmaybe-uninitialized]
753 | if (idid <= 0) {
| ^~
par_solve.cpp:746:7: note: 'idid' was declared here
746 | int idid, itol=0;
| ^~~~
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c prja.c -o prja.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c rprintf.c -o rprintf.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/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-dev/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c rxData.cpp -o rxData.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/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-dev/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c rxInv.cpp -o rxInv.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/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-dev/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c rxOptRep.cpp -o rxOptRep.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/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-dev/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c rxode2_df.cpp -o rxode2_df.o
In file included from rxode2_df.cpp:33:
/data/gannet/ripley/R/test-dev/rxode2parse/include/rxode2parseGetTime.h: In function 'int handleInfusionStartRm(int*, int*, double*, int*, rx_solve*, rx_solving_options*, rx_solving_options_ind*)':
/data/gannet/ripley/R/test-dev/rxode2parse/include/rxode2parseGetTime.h:223:9: warning: unused variable 'curEvid' [-Wunused-variable]
223 | int curEvid = getEvid(ind, ind->idose[*endIdx+1]);
| ^~~~~~~
In function 'double handleInfusionItem(int, rx_solve*, rx_solving_options*, rx_solving_options_ind*)',
inlined from 'double getTime__(int, rx_solving_options_ind*, int)' at /data/gannet/ripley/R/test-dev/rxode2parse/include/rxode2parseGetTime.h:381:34:
/data/gannet/ripley/R/test-dev/rxode2parse/include/rxode2parseGetTime.h:314:5: warning: 'infBidx' may be used uninitialized [-Wmaybe-uninitialized]
314 | if (infBidx == -1) return 0.0;
| ^~
/data/gannet/ripley/R/test-dev/rxode2parse/include/rxode2parseGetTime.h: In function 'double getTime__(int, rx_solving_options_ind*, int)':
/data/gannet/ripley/R/test-dev/rxode2parse/include/rxode2parseGetTime.h:312:9: note: 'infBidx' was declared here
312 | int infBidx;
| ^~~~~~~
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/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-dev/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c rxode2parse.cpp -o rxode2parse.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/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-dev/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c rxode2random.cpp -o rxode2random.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c sbuf.c -o sbuf.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c scaleh.c -o scaleh.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c solsy.c -o solsy.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c stoda.c -o stoda.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c strdup_printf.c -o strdup_printf.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c strncmp.c -o strncmp.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c utilc.c -o utilc.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/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-dev/BH/include" -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c utilcpp.cpp -o utilcpp.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/rxode2parse/include' -I'/data/gannet/ripley/R/test-dev/rxode2random/include' -I'/data/gannet/ripley/R/test-dev/PreciseSums/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -D_isrxode2_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c vmnorm.c -o vmnorm.o
g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -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 -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/rxode2/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/rxode2/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/rxode2/src'
installing via 'install.libs.R' to /data/gannet/ripley/R/packages/tests-devel/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)