- using R Under development (unstable) (2024-06-14 r86745)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-14 (GCC) 14.1.0
GNU Fortran (GCC) 14.1.0
- running under: Fedora Linux 36 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- checking for file ‘VAJointSurv/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘VAJointSurv’ version ‘0.1.0’
- 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 ‘VAJointSurv’ can be installed ... [627s/254s] OK
See the install log for details.
- used C++ compiler: ‘g++-14 (GCC) 14.1.0’
- checking C++ specification ... OK
- 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 ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... OK
- checking loading without being on the library search path ... 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 ... [20s/25s] OK
- checking Rd files ... 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 $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compilation flags used ... OK
- checking compiled code ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [91s/89s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [5s/11s] ERROR
Running ‘testthat.R’ [5s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(VAJointSurv)
Loading required package: survival
>
> options(testthat.progress.max_fails = 1000)
> test_check("VAJointSurv")
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: eval_expansion(ptr, x, weights, der, lower_limit)
2: obj_cpp$eval(out_x)
3: eval(code, test_env)
4: eval(code, test_env)
5: 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)
6: doTryCatch(return(expr), name, parentenv, handler)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: 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) { })
13: test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter())
14: test_that("The C++ version of poly gives the right result", { in_x <- 2:5 obj_truth <- poly(in_x, degree = 3) out_x <- 1:6 truth <- predict(obj_truth, out_x) obj_cpp <- poly_term(in_x, degree = 3) expect_s3_class(obj_cpp, "poly_term") expect_equal(obj_cpp$time, in_x) expansion <- obj_cpp$eval(out_x) expect_equal(expansion, t(truth), ignore_attr = TRUE) obj_cpp <- poly_term(in_x, degree = 3, intercept = TRUE) expect_s3_class(obj_cpp, "poly_term") expect_equal(obj_cpp$time, in_x) expansion <- obj_cpp$eval(out_x) expect_equal(expansion, rbind(1, t(truth)), ignore_attr = TRUE) obj_cpp <- poly_term(in_x, degree = 3, raw = TRUE) expect_s3_class(obj_cpp, "poly_term") expect_equal(obj_cpp$time, in_x) expansion <- obj_cpp$eval(out_x) expect_equal(expansion, t(outer(out_x, 1:3, `^`))) obj_cpp <- poly_term(in_x, degree = 3, raw = TRUE, intercept = TRUE) expect_s3_class(obj_cpp, "poly_term") expect_equal(obj_cpp$time, in_x) expansion <- obj_cpp$eval(out_x) expect_equal(expansion, t(outer(out_x, 0:3, `^`))) obj_cpp <- poly_term(in_x, degree = 0) expect_s3_class(obj_cpp, "poly_term") expect_equal(obj_cpp$time, in_x) expansion <- obj_cpp$eval(out_x) expect_equal(expansion, matrix(0, 0, length(out_x))) obj_cpp <- poly_term(in_x, degree = 0, intercept = TRUE) expect_s3_class(obj_cpp, "poly_term") expect_equal(obj_cpp$time, in_x) expansion <- obj_cpp$eval(out_x) expect_equal(expansion, matrix(1, 1, length(out_x)))})
15: eval(code, test_env)
16: eval(code, test_env)
17: 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)
18: doTryCatch(return(expr), name, parentenv, handler)
19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
20: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: 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) { })
25: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
26: source_file(path, env = env(env), desc = desc, error_call = error_call)
27: FUN(X[[i]], ...)
28: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
29: doTryCatch(return(expr), name, parentenv, handler)
30: tryCatchOne(expr, names, parentenv, handlers[[1L]])
31: tryCatchList(expr, classes, parentenv, handlers)
32: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
33: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
34: 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)
35: 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)
36: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
37: test_check("VAJointSurv")
An irrecoverable exception occurred. R is aborting now ...
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [13s/16s] OK
- checking PDF version of manual ... [8s/12s] OK
- checking HTML version of manual ... OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 1 ERROR