• using R Under development (unstable) (2024-12-18 r87448)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.5 (1)     Debian flang-new version 19.1.5 (1)
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘LOMAR/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘LOMAR’ version ‘0.5.0’
• 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 ‘LOMAR’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘Debian clang version 19.1.5 (1)’
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [0s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the package can be unloaded cleanly ... [0s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
• checking loading without being on the library search path ... [0s/1s] OK
• checking use of S3 registration ... 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 ... [14s/19s] OK
• checking Rd files ... [1s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... 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 use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking examples ... [15s/25s] OK Examples with CPU (user + system) or elapsed time > 5s        user system elapsed jrmpc 8.913 0.106 11.473
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [14s/161s] ERROR   Running ‘testthat.R’ [13s/161s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > suppressPackageStartupMessages(library(LOMAR))   >   > test_check("LOMAR")       *** caught segfault ***   address 0x1, cause 'memory not mapped'      Traceback:    1: `[.ff_array`(A, )    2: A[]    3: circle_hough_transform(img, rmin = 5, rmax = 5, threshold = 0.4)    4: eval(code, test_env)    5: eval(code, test_env)    6: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)    7: doTryCatch(return(expr), name, parentenv, handler)    8: tryCatchOne(expr, names, parentenv, handlers[[1L]])    9: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])   10: doTryCatch(return(expr), name, parentenv, handler)   11: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])   12: tryCatchList(expr, classes, parentenv, handlers)   13: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })   14: test_code(desc, code, env = parent.frame(), reporter = reporter)   15: test_that("Circle Hough transform works", { I <- points2img(points = as.data.frame(PS[[2]]), voxel.size = c(10, 10, 30), method = "histogram") img <- apply(I, c(1, 2), sum) df <- circle_hough_transform(img, rmin = 5, rmax = 5, threshold = 0.4) expect_equal(df[, c("x", "y", "r")], data.frame(x = 16, y = 12, r = 5))})   16: eval(code, test_env)   17: eval(code, test_env)   18: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)   19: doTryCatch(return(expr), name, parentenv, handler)   20: tryCatchOne(expr, names, parentenv, handlers[[1L]])   21: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])   22: doTryCatch(return(expr), name, parentenv, handler)   23: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])   24: tryCatchList(expr, classes, parentenv, handlers)   25: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })   26: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())   27: source_file(path, env = env(env), desc = desc, error_call = error_call)   28: FUN(X[[i]], ...)   29: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)   30: doTryCatch(return(expr), name, parentenv, handler)   31: tryCatchOne(expr, names, parentenv, handlers[[1L]])   32: tryCatchList(expr, classes, parentenv, handlers)   33: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})   34: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))   35: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call)   36: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel)   37: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")   38: test_check("LOMAR")   An irrecoverable exception occurred. R is aborting now ...   Segmentation fault
• checking PDF version of manual ... [5s/7s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR