Closed mattfidler closed 4 months ago
Dear maintainer,
Please see the problems shown on https://cran.r-project.org/web/checks/check_results_rxode2.html.
Please correct before 2024-06-10 to safely retain your package on CRAN.
Best, -k
* installing *source* package ‘rxode2’ ... ** package ‘rxode2’ successfully unpacked and MD5 sums checked ** using staged installation R Under development (unstable) (2024-04-13 r86413) -- "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 > 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 0.796 0.091 1.332 --------[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[2]: Entering directory '/data/gannet/ripley/R/packages/tests-noRemap/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 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:30, from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25, from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29, from RcppExports.cpp:2: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/r/headers.h:26: warning: "R_NO_REMAP" redefined 26 | #define R_NO_REMAP | <command-line>: note: this is the location of the previous definition 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 -DR_NO_REMAP -c boost.cpp -o boost.o In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:30, from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25, from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29, from boost.cpp:15: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/r/headers.h:26: warning: "R_NO_REMAP" redefined 26 | #define R_NO_REMAP | <command-line>: note: this is the location of the previous definition 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 -DR_NO_REMAP -c etTran.cpp -o etTran.o In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:30, from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25, from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29, from etTran.cpp:6: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/r/headers.h:26: warning: "R_NO_REMAP" redefined 26 | #define R_NO_REMAP | <command-line>: note: this is the location of the previous definition 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 -DR_NO_REMAP -c expandGrid.cpp -o expandGrid.o In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:30, from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:27, from expandGrid.cpp:6: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/r/headers.h:26: warning: "R_NO_REMAP" redefined 26 | #define R_NO_REMAP | <command-line>: note: this is the location of the previous definition 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 -DR_NO_REMAP -c expm.cpp -o expm.o In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:30, from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25, from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29, from expm.cpp:6: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/r/headers.h:26: warning: "R_NO_REMAP" redefined 26 | #define R_NO_REMAP | <command-line>: note: this is the location of the previous definition 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 -DR_NO_REMAP -c forder.cpp -o forder.o forder.cpp: In function 'SEXPREC* getRxThreads_R(SEXP)': forder.cpp:102:8: error: 'isLogical' was not declared in this scope; did you mean 'Rf_isLogical'? 102 | if (!isLogical(verbose) || LENGTH(verbose)!=1 || INTEGER(verbose)[0]==NA_LOGICAL) | ^~~~~~~~~ | Rf_isLogical forder.cpp:122:10: error: 'ScalarInteger' was not declared in this scope; did you mean 'Rf_ScalarInteger'? 122 | return ScalarInteger(getRxThreads(INT_MAX, false)); | ^~~~~~~~~~~~~ | Rf_ScalarInteger forder.cpp: In function 'SEXPREC* setRxthreads(SEXP, SEXP, SEXP)': forder.cpp:126:7: error: 'length' was not declared in this scope 126 | if (length(throttle)) { | ^~~~~~ forder.cpp:127:10: error: 'isInteger' was not declared in this scope; did you mean 'Rf_isInteger'? 127 | if (!isInteger(throttle) || LENGTH(throttle)!=1 || INTEGER(throttle)[0]<1) | ^~~~~~~~~ | Rf_isInteger forder.cpp:128:7: error: 'error' was not declared in this scope; did you mean 'perror'? 128 | error("%s", _("'throttle' must be a single number, non-NA, and >=1")); | ^~~~~ | perror forder.cpp:132:8: error: 'length' was not declared in this scope 132 | if (!length(threads) && !length(throttle)) { | ^~~~~~ forder.cpp:141:32: error: 'isInteger' was not declared in this scope; did you mean 'Rf_isInteger'? 141 | if (length(threads)!=1 || !isInteger(threads) || (n=INTEGER(threads)[0]) < 0) { // <0 catches NA too since NA is negative (INT_MIN) | ^~~~~~~~~ | Rf_isInteger forder.cpp:145:10: error: 'isLogical' was not declared in this scope; did you mean 'Rf_isLogical'? 145 | if (!isLogical(percent) || length(percent)!=1 || LOGICAL(percent)[0]==NA_LOGICAL) { | ^~~~~~~~~ | Rf_isLogical forder.cpp:149:25: error: 'error' was not declared in this scope; did you mean 'perror'? 149 | if (n<2 || n>100) error(_("internal error: threads==%d should be between 2 and 100 (percent=TRUE at C level)"), n); // # nocov | ^~~~~ | perror forder.cpp:163:10: error: 'ScalarInteger' was not declared in this scope; did you mean 'Rf_ScalarInteger'? 163 | return ScalarInteger(old); | ^~~~~~~~~~~~~ | Rf_ScalarInteger make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:202: forder.o] Error 1 make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-noRemap/rxode2/src' ERROR: compilation failed for package ‘rxode2’ * removing ‘/data/gannet/ripley/R/packages/tests-noRemap/Libs/rxode2-lib/rxode2’ Command exited with non-zero status 1 Time 2:25.75, 131.76 + 9.31
Dear maintainer,
Please see the problems shown on https://cran.r-project.org/web/checks/check_results_rxode2.html.
Please correct before 2024-06-10 to safely retain your package on CRAN.
Best, -k