CRAN Package Check Results for Package dynamichazard

Last updated on 2018-11-17 09:46:47 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.6.1 425.27 196.51 621.78 OK
r-devel-linux-x86_64-debian-gcc 0.6.1 373.43 151.33 524.76 OK
r-devel-linux-x86_64-fedora-clang 0.6.1 922.71 NOTE
r-devel-linux-x86_64-fedora-gcc 0.6.1 847.86 OK
r-devel-windows-ix86+x86_64 0.6.1 1108.00 397.00 1505.00 NOTE
r-patched-linux-x86_64 0.6.1 459.23 187.71 646.94 OK
r-patched-solaris-x86 0.6.1 782.40 ERROR
r-release-linux-x86_64 0.6.1 444.71 188.33 633.04 OK
r-release-windows-ix86+x86_64 0.6.1 1117.00 387.00 1504.00 NOTE
r-release-osx-x86_64 0.6.1 NOTE
r-oldrel-windows-ix86+x86_64 0.6.1 1096.00 423.00 1519.00 NOTE
r-oldrel-osx-x86_64 0.6.1 NOTE

Check Details

Version: 0.6.1
Check: installed package size
Result: NOTE
     installed size is 29.1Mb
     sub-directories of 1Mb or more:
     data 4.2Mb
     doc 1.3Mb
     libs 23.1Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.6.1
Check: tests
Result: ERROR
     Running ‘testthat.R’ [15s/40s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > # Had the same issue as in this thread: https://github.com/hadley/testthat/issues/86
     > Sys.setenv("R_TESTS" = "")
     >
     > options(deparse.max.lines = 5)
     >
     > testthat::test_check("dynamichazard", reporter = "summary")
     Loading required package: dynamichazard
     Loading required package: survival
     Tracing function "expect_known_value" in package "testthat"
     Tracing function "expect_known_output" in package "testthat"
     Loading required package: DBI
     Running tests for GMA: ..................
     Testing LAPACK wrapper functions: ..........................................
     Running test_PF: ........................................................................................................................................................................................................SS...SSSSSSS..S
     *** caught segfault ***
     address 0, cause 'memory not mapped'
    
     Traceback:
     1: PF_smooth(n_fixed_terms_in_state_vec = static_args$n_fixed_terms_in_state_vec, X = static_args$X, fixed_terms = static_args$fixed_terms, tstart = static_args$tstart, tstop = static_args$tstop, Q_0 = 0.2000200020002, Q = 0.2, a_0 = 0, R = model_args$R, risk_obj = static_args$risk_obj, n_max = control$n_max, n_threads = control$n_threads, N_fw_n_bw = control$N_fw_n_bw, ...
     2: eval(fit_call, envir = parent.frame())
     3: eval(fit_call, envir = parent.frame())
     4: .PF_EM(trace = trace, seed = seed, fixed_parems = fixed_parems, type = type, n_fixed_terms_in_state_vec = static_args$n_fixed_terms_in_state_vec, X = static_args$X, fixed_terms = static_args$fixed_terms, tstart = static_args$tstart, tstop = static_args$tstop, risk_obj = static_args$risk_obj, debug = static_args$debug, model = static_args$model, Q = model_args$Q, ...
     5: PF_EM(Surv(start, stop, event) ~ ddFixed(group) + ddFixed_intercept(TRUE), head_neck_cancer, Q_0 = 1, Q = 0.2, Fmat = diag(0.01, 1), by = 1, type = "VAR", model = "logit", max_T = 30, control = PF_control(N_fw_n_bw = 50, N_smooth = 100, N_first = 500, eps = 0.001, method = "AUX_normal_approx_w_cloud_mean", n_max = 2, smoother = "Fearnhead_O_N", Q_tilde = diag(0.3^2, ...
     6: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
     7: suppressWarnings(PF_EM(Surv(start, stop, event) ~ ddFixed(group) + ddFixed_intercept(TRUE), head_neck_cancer, Q_0 = 1, Q = 0.2, Fmat = diag(0.01, 1), by = 1, type = "VAR", model = "logit", max_T = 30, control = PF_control(N_fw_n_bw = 50, N_smooth = 100, N_first = 500, eps = 0.001, method = "AUX_normal_approx_w_cloud_mean", ...
     8: eval(code, test_env)
     9: eval(code, test_env)
     10: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() } ...
     11: doTryCatch(return(expr), name, parentenv, handler)
     12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     13: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     14: doTryCatch(return(expr), name, parentenv, handler)
     15: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     16: tryCatchList(expr, classes, parentenv, handlers)
     17: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() } ...
     18: test_code(desc, code, env = parent.frame())
     19: test_that("type = 'VAR' works with non-zero mean for with a single term and gives previous results", { set.seed(30520116) pf_Fear <- suppressWarnings(PF_EM(Surv(start, stop, event) ~ ddFixed(group) + ddFixed_intercept(TRUE), head_neck_cancer, ...
     20: eval(code, test_env)
     21: eval(code, test_env)
     22: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() } ...
     23: doTryCatch(return(expr), name, parentenv, handler)
     24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     25: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     26: doTryCatch(return(expr), name, parentenv, handler)
     27: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     28: tryCatchList(expr, classes, parentenv, handlers)
     29: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() } ...
     30: test_code(NULL, exprs, env)
     31: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
     32: force(code)
     33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter, { lister$start_file(basename(path)) source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap) ...
     34: FUN(X[[i]], ...)
     35: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
     36: force(code)
     37: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap))
     38: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
     39: test_dir(path = test_path, reporter = reporter, env = env, filter = filter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
     40: test_package_dir(package = package, test_path = test_path, filter = filter, reporter = reporter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
     41: testthat::test_check("dynamichazard", reporter = "summary")
     An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86