* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘rxode2et’ ...
** package ‘rxode2et’ successfully unpacked and MD5 sums checked
** using staged installation
R version 4.4.0 Patched (2024-04-30 r86503) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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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.
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> ## This is only for rxode2
> .in <- suppressWarnings(readLines("src/Makevars.in"))
>
> if (.Platform$OS.type == "windows" && !file.exists("src/Makevars.win")) {
+ .in <- gsub("@CXX14STD@", "-std=c++1y", .in)
+ file.out <- file("src/Makevars.win", "wb")
+ writeLines(gsub("@ISYSTEM@", "I", .in),
+ file.out)
+ close(file.out)
+ } else {
+ .in <- gsub("@CXX14STD@", "-std=gnu++14", .in)
+ file.out <- file("src/Makevars", "wb")
+ writeLines(gsub("@ISYSTEM@", "isystem", .in),
+ file.out)
+ close(file.out)
+ }
>
> if (file.exists("man/reexports.Rd")) {
+ l <- readLines("man/reexports.Rd")
+ if (!any(regexpr("[\\]value", l) != -1)) {
+ l <- c(l, "\\value{ Inherited from parent routine }")
+ file.out <- file("man/reexports.Rd", "wb")
+ writeLines(l, file.out)
+ close(file.out)
+ }
+ }
>
>
> unlink("R/rxode2_md5.R")
>
> cpp <- list.files("src", pattern = ".(c|h|cpp|f)$")
> #Rfiles <- list.files("R/", pattern = ".R")
>
> cmd <- file.path(R.home("bin"), "R")
> args <- c("CMD", "config")
>
> md5 <- digest::digest(c(lapply(c(paste0("src/", cpp)#,
+ #paste0("inst/include/", include)#,
+ #paste0("R/", Rfiles)
+ ), digest::digest, file = TRUE),
+ ## vapply(c("BLAS_LIBS", "CC", "CFLAGS", "CPICFLAGS",
+ ## "CXX", "CXXFLAGS", "CXXPICFLAGS",
+ ## "CXX11", "CXX11STD", "CXX11FLAGS", "CXX11PICFLAGS",
+ ## "CXX14", "CXX14STD", "CXX14FLAGS", "CXX14PICFLAGS",
+ ## "CXX17", "CXX17STD", "CXX17FLAGS", "CXX17PICFLAGS",
+ ## "CXX20", "CXX20STD", "CXX20FLAGS", "CXX20PICFLAGS",
+ ## "FC", "FFLAGS", "FCFLAGS", "FPICFLAGS"),
+ ## function(cfg) {
+ ## rawToChar(sys::exec_internal(cmd, c(args, cfg))$stdout)
+ ## }, character(1)
+ ## ),
+ ""
+ ))
> unlink("R/rxode2et_md5.R")
> md5file <- file("R/rxode2et_md5.R", "wb")
> writeLines(sprintf("rxode2et.md5 <- \"%s\"\n", md5), md5file)
> close(md5file)
>
> l <- readLines(file.path(system.file(package="rxode2random"), "include", "rxode2random_as.h"))
> l <- gsub("qtest", "_rxode2et_qtest", l)
>
> rxode2et_as.h <- file("src/rxode2et_as.h", "wb")
> writeLines(l, rxode2et_as.h)
> close(rxode2et_as.h)
>
> proc.time()
user system elapsed
0.255 0.077 0.315
--------[begin src/Makevars]--------
# -*- mode: makefile-gmake -*-
################################################################################
## Package library flags.
PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS)
# Release options
PKG_CFLAGS = -D_isrxode2et_
PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -D_isrxode2et_
--------[end src/Makevars]--------
--------[begin R/rxode2et_md5.R]--------
rxode2et.md5 <- "e66f5422096c8f3ded6ff79d6fcddac8"
--------[begin R/rxode2et_md5.R]--------
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-23) 13.2.0’
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/tmp/RtmpysWFV7/R.INSTALLca3007afd8ffa/rxode2et/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -D_isrxode2et_ -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -D_isrxode2et_ -fpic -g -O2 -Wall -pedantic -mtune=native -c cbindThetaOmega.cpp -o cbindThetaOmega.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -D_isrxode2et_ -fpic -g -O2 -Wall -pedantic -mtune=native -c et.cpp -o et.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -D_isrxode2et_ -fpic -g -O2 -Wall -pedantic -mtune=native -c etTran.cpp -o etTran.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2et_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -D_isrxode2et_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c isEt.c -o isEt.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -D_isrxode2et_ -fpic -g -O2 -Wall -pedantic -mtune=native -c rxStack.cpp -o rxStack.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2random/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rxode2parse/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -D_isrxode2et_ -fpic -g -O2 -Wall -pedantic -mtune=native -c rxode2random.cpp -o rxode2random.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o rxode2et.so RcppExports.o cbindThetaOmega.o et.o etTran.o init.o isEt.o rxStack.o rxode2random.o -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpysWFV7/R.INSTALLca3007afd8ffa/rxode2et/src'
make[1]: Entering directory '/tmp/RtmpysWFV7/R.INSTALLca3007afd8ffa/rxode2et/src'
make[1]: Leaving directory '/tmp/RtmpysWFV7/R.INSTALLca3007afd8ffa/rxode2et/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-rxode2et/00new/rxode2et/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘rxode2et’
finding HTML links ... done
add.dosing html
add.sampling html
as.et html
dot-clearPipe html
dot-collectWarnings html
dot-pipeRx html
dot-s3register html
dot-setRxode2 html
et html
etExpand html
etRbind html
etRep html
etSeq html
eventTable html
forderForceBase html
is.rxEt html
is.rxStackData html
reexports html
rxCbindStudyIndividual html
rxEtDispatchSolve html
rxEvid html
rxRateDur html
rxReq html
rxStack html
toTrialDuration html
** building package indices
** 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 (rxode2et)