* 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 4.4.1 Patched (2024-07-08 r86886) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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Type 'license()' or 'licence()' for distribution details.

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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 
  0.196   0.036   0.220 
--------[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 <- "f3801ebf6c12354dcbe005e51737da8c"

--------[begin R/rxode2et_md5.R]--------
** libs
using C compiler: ‘gcc-13 (Debian 13.3.0-1) 13.3.0’
using C++ compiler: ‘g++-13 (Debian 13.3.0-1) 13.3.0’
make[1]: Entering directory '/tmp/RtmpzAzBgn/R.INSTALL1f0de7631bdfe1/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
et.cpp: In function ‘Rcpp::List etSort(Rcpp::List&)’:
et.cpp:488:8: warning: unused variable ‘naTime’ [-Wunused-variable]
  488 |   bool naTime=false;
      |        ^~~~~~
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/RtmpzAzBgn/R.INSTALL1f0de7631bdfe1/rxode2et/src'
make[1]: Entering directory '/tmp/RtmpzAzBgn/R.INSTALL1f0de7631bdfe1/rxode2et/src'
make[1]: Leaving directory '/tmp/RtmpzAzBgn/R.INSTALL1f0de7631bdfe1/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)