* installing *source* package ‘rxode2et’ ... ** package ‘rxode2et’ 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 > .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 0.344 0.079 0.666 --------[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: ‘clang version 18.1.4’ using C++ compiler: ‘clang version 18.1.4’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rxode2et/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/rxode2random/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2et_ -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.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/rxode2random/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2et_ -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c cbindThetaOmega.cpp -o cbindThetaOmega.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/rxode2random/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2et_ -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c et.cpp -o et.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/rxode2random/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2et_ -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c etTran.cpp -o etTran.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/rxode2random/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_isrxode2et_ -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/rxode2random/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -D_isrxode2et_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c isEt.c -o isEt.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/rxode2random/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2et_ -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c rxStack.cpp -o rxStack.o rxStack.cpp:57:7: warning: variable 'ncols' set but not used [-Wunused-but-set-variable] 57 | int ncols=3; | ^ 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/rxode2random/include' -I'/data/gannet/ripley/R/test-clang/rxode2parse/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -D_isrxode2et_ -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c rxode2random.cpp -o rxode2random.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 rxode2et.so RcppExports.o cbindThetaOmega.o et.o etTran.o init.o isEt.o rxStack.o rxode2random.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 make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rxode2et/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rxode2et/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rxode2et/src' installing to /data/gannet/ripley/R/packages/tests-clang/rxode2et.Rcheck/00LOCK-rxode2et/00new/rxode2et/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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)