* 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 (2024-08-05 r86980) -- "Race for Your Life" 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 > .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 0.222 0.026 0.235 --------[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-14 (Debian 14.2.0-1) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-1) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp8c2Ntl/R.INSTALL1030015423c22/rxode2et/src' g++-14 -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++-14 -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++-14 -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++-14 -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-14 -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-14 -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++-14 -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++-14 -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++-14 -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 '/home/hornik/tmp/scratch/Rtmp8c2Ntl/R.INSTALL1030015423c22/rxode2et/src' make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp8c2Ntl/R.INSTALL1030015423c22/rxode2et/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp8c2Ntl/R.INSTALL1030015423c22/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)