Check results for 'RTMB'

using R Under development (unstable) (2026-02-12 r89409)
using platform: aarch64-apple-darwin23
R was compiled by Apple clang version 17.0.0 (clang-1700.3.19.1) GNU Fortran (GCC) 14.2.0
running under: macOS Sequoia 15.7.1
using session charset: UTF-8 * current time: 2026-02-13 02:01:06 UTC
checking for file ‘RTMB/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘RTMB’ version ‘1.8’
package encoding: UTF-8
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking whether package ‘RTMB’ can be installed ... [127s/39s] OK See the install log for details.
used C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.3.19.1)’
used SDK: ‘MacOSX14.5.sdk’
checking installed package size ... INFO installed size is 140.4Mb sub-directories of 1Mb or more: R 2.0Mb libs 137.5Mb
checking package directory ... OK
checking ‘build’ directory ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking code files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [1s/1s] OK
checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
checking whether the package can be unloaded cleanly ... [1s/1s] OK
checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
checking loading without being on the library search path ... [1s/1s] OK
checking dependencies in R code ... OK
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... [3s/3s] OK
checking Rd files ... [0s/0s] OK
checking Rd metadata ... OK
checking Rd cross-references ... OK
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking line endings in C/C++/Fortran sources/headers ... OK
checking line endings in Makefiles ... OK
checking compilation flags in Makevars ... OK
checking for GNU extensions in Makefiles ... OK
checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
checking use of PKG_*FLAGS in Makefiles ... OK
checking compiled code ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [1s/1s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [0s/1s] ERROR Running ‘tinytest.R’ [0s/1s] Running the tests in ‘tests/tinytest.R’ failed. Complete output: > if (requireNamespace("tinytest", quietly=TRUE)) { + tinytest::test_package("RTMB", ncpu=getOption("Ncpus", 1)) + } starting worker pid=56958 on localhost:11773 at 15:02:07.770 test-advector.R............... 9 tests [0;32mOK [0m [0;36m23ms [0m test-bessel.R................. 6 tests [0;32mOK [0m [0;36m7ms [0m test-distributions.R.......... 18 tests [0;32mOK [0m [0;34m0.5s [0m *** caught segfault *** address 0x1, cause 'invalid permissions' Traceback: 1: eigen(x, symmetric = TRUE) 2: eigen(x, symmetric = TRUE) 3: matlog(x + (1 - diag(5)) * AD(0+1i) + diag(5) * 2) 4: f(x) 5: mode(current) 6: attr.all.equal(target, current, tolerance = tolerance, scale = scale, ...) 7: all.equal.numeric(target, current, tolerance = tolerance, ...) 8: all.equal(target, current, tolerance = tolerance, ...) 9: fun(...) 10: expect_equal(f(x), F(x), info = "symmetric complex eigen") 11: eval(expr, envir = e) 12: eval(expr, envir = e) 13: FUN(X[[i]], ...) 14: (function (X, FUN, ...) { FUN <- match.fun(FUN) if (!is.vector(X) || is.object(X)) X <- as.list(X) .Internal(lapply(X, FUN))})(base::quote(c("/Volumes/Builds/packages/sonoma-arm64/results/4.6/RTMB.Rcheck/RTMB/tinytest/test-advector.R", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/RTMB.Rcheck/RTMB/tinytest/test-bessel.R", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/RTMB.Rcheck/RTMB/tinytest/test-distributions.R", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/RTMB.Rcheck/RTMB/tinytest/test-factorize.R", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/RTMB.Rcheck/RTMB/tinytest/test-model-spatial.R", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/RTMB.Rcheck/RTMB/tinytest/test-model-spde.R", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/RTMB.Rcheck/RTMB/tinytest/test-sparse.R", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/RTMB.Rcheck/RTMB/tinytest/test-spline.R", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/RTMB.Rcheck/RTMB/tinytest/test-tape.R")), FUN = base::quote(function (file, at_home = TRUE, verbose = getOption("tt.verbose", 2), color = getOption("tt.pr.color", TRUE), remove_side_effects = TRUE, side_effects = FALSE, set_env = list(), encoding = "unknown", ...) { if (!file_test("-f", file)) { stop(sprintf("'%s' does not exist or is a directory", file), call. = FALSE) } t0 <- Sys.time() if (length(set_env) > 0) { old_env_var <- sapply(names(set_env), Sys.getenv, unset = NA_character_, USE.NAMES = TRUE) do.call(Sys.setenv, set_env) } oldwd <- getwd() set_call_wd(oldwd) grDevices::pdf(file = nullfile()) envvar <- new.env() oldop <- new.env() locale <- Sys.getlocale() on.exit({ setwd(oldwd) set_call_wd("") Sys.unsetenv("TT_AT_HOME") if (remove_side_effects) { unset_envvar(envvar) reset_options(oldop) reset_locale(locale) } grDevices::dev.off() if (exists("old_env_var")) { unset <- is.na(old_env_var) Sys.unsetenv(names(old_env_var)[unset]) if (any(!unset)) do.call(Sys.setenv, as.list(old_env_var)[!unset]) } }) setwd(dirname(file)) file <- basename(file) if (at_home) Sys.setenv(TT_AT_HOME = TRUE) o <- output() e <- new.env(parent = globalenv()) add_locally_masked_functions(envir = e, output = o) e$Sys.setenv <- capture_envvar(Sys.setenv, envvar) e$options <- capture_options(options, oldop) options(useFancyQuotes = FALSE) Sys.setenv(R_TESTS = "") sidefx <- new.env() e$report_side_effects <- capture_se(report_side_effects, sidefx) do.call(e$report_side_effects, as.list(side_effects)) local_report_envvar <- capture(report_envvar, o) local_report_cwd <- capture(report_cwd, o) local_report_files <- capture(report_files, o) local_report_locale <- capture(report_locale, o) check_double_colon(filename = file) parsed <- parse(file = file, keep.source = TRUE, encoding = encoding) src <- attr(parsed, "srcref") o$file <- file prfile <- basename(file) if (nchar(prfile) > 30) { prfile <- paste0("..", substr(prfile, nchar(prfile) - 27, nchar(prfile))) } prfile <- gsub(" ", ".", sprintf("%-30s", basename(file))) for (i in seq_along(parsed)) { expr <- parsed[[i]] o$fst <- src[[i]][1] o$lst <- src[[i]][3] o$call <- expr if (!o$exit) eval(expr, envir = e) else break local_report_envvar(sidefx) local_report_cwd(sidefx) local_report_files(sidefx) local_report_locale(sidefx) if (verbose == 2) print_status(prfile, o, color, print = TRUE) } td <- abs(Sys.time() - t0) tx <- humanize(td, color = color) if (verbose == 1) { str <- print_status(prfile, o, color, print = FALSE) if (o$exit) catf("%s %s %s\n", str, tx, o$exit_msg()) else catf("%s %s\n", str, tx) } if (verbose >= 2) { str <- if (o$exit) catf("%s %s\n", tx, o$exit_msg()) else catf("%s\n", tx) } test_output <- o$gimme() structure(test_output, class = "tinytests", duration = td)}), at_home = base::quote(FALSE), verbose = base::quote(1), color = base::quote(TRUE), remove_side_effects = base::quote(TRUE)) 15: do.call(msg$data$fun, msg$data$args, quote = TRUE) 16: doTryCatch(return(expr), name, parentenv, handler) 17: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 18: tryCatchList(expr, classes, parentenv, handlers) 19: tryCatch(do.call(msg$data$fun, msg$data$args, quote = TRUE), error = handler) 20: doTryCatch(return(expr), name, parentenv, handler) 21: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 22: tryCatchList(expr, classes, parentenv, handlers) 23: tryCatch({ msg <- recvData(master) if (msg$type == "DONE") { closeNode(master) FALSE } else if (msg$type == "EXEC") { success <- TRUE handler <- function(e) { success <<- FALSE structure(conditionMessage(e), class = c("snow-try-error", "try-error")) } t1 <- proc.time() value <- tryCatch(do.call(msg$data$fun, msg$data$args, quote = TRUE), error = handler) t2 <- proc.time() value <- list(type = "VALUE", value = value, success = success, time = t2 - t1, tag = msg$data$tag) msg <- NULL sendData(master, value) value <- NULL TRUE } else { TRUE }}, interrupt = function(e) TRUE) 24: workCommand(master) 25: workLoop(makeSOCKmaster(master, port, setup_timeout, timeout, useXDR, setup_strategy)) 26: tryCatch(parallel:::.workRSOCK, error = function(e) parallel:::.slaveRSOCK)() An irrecoverable exception occurred. R is aborting now ... Error in unserialize(node$con) : error reading from connection Calls: <Anonymous> ... FUN -> recvData -> recvData.SOCKnode -> unserialize Execution halted
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [6s/6s] OK
checking PDF version of manual ... [3s/3s] OK
DONE Status: 1 ERROR
using check arguments '--no-clean-on-error '