Last updated on 2024-11-23 09:49:56 CET.
| Package | ERROR | OK |
|---|---|---|
| free | 13 | |
| ktweedie | 13 | |
| sox | 1 | 12 |
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: ERROR: 1, OK: 12
Version: 1.2
Check: examples
Result: ERROR
Running examples in ‘sox-Ex.R’ failed
The error most likely occurred in:
> ### Name: plot.sox
> ### Title: Solution path plot for 'sox()'
> ### Aliases: plot.sox
>
> ### ** Examples
>
> x <- as.matrix(sim[, c("A1","A2","C1","C2","B","A1B","A2B","C1B","C2B")])
> lam.seq <- exp(seq(log(1e0), log(1e-3), length.out = 20))
>
> overlapping.groups <- list(c(1, 2, 6, 7),
+ c(5, 6, 7, 8, 9),
+ c(6, 7),
+ c(3, 4, 8, 9),
+ c(8, 9))
>
> pars.overlapping <- overlap_structure(overlapping.groups)
>
> fit.overlapping <- sox(
+ x = x,
+ ID = sim$Id,
+ time = sim$Start,
+ time2 = sim$Stop,
+ event = sim$Event,
+ penalty = "overlapping",
+ lambda = lam.seq,
+ group = pars.overlapping$groups,
+ group_variable = pars.overlapping$groups_var,
+ penalty_weights = pars.overlapping$group_weights,
+ tol = 1e-4,
+ maxit = 1e3,
+ verbose = FALSE
+ )
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: coxph.wtest(fit$var[nabeta, nabeta], temp, control$toler.chol)
2: coxph(Surv(Start, Stop, Event) ~ x, init = beta, control = list(iter.max = 0, timefix = FALSE))
3: (function (beta, x, n, Start, Stop, Event) { fit.cox <- coxph(Surv(Start, Stop, Event) ~ x, init = beta, control = list(iter.max = 0, timefix = FALSE)) l <- -fit.cox$loglik[1]/n ld <- -fit.cox$first/n return(c(l, ld))})(c(0, 0, 0, 0, 0, 0, 0, 0, 0), c(1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 0, 1, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 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4: sox_cpp(x = x, start = time, stop = time2, event = event, n_unique = n, regul = regul, lam = lambdas, grp = group, grpV = group_variable, own_var = own_variable, N_own_var = no_own_variable, etaG = penalty_weights, init = par_init, l_ld = l_ld, init_stepsize = stepsize_init, ls_shrink = stepsize_shrink, partol = tol, maxit = maxit, verbose = verbose)
5: sox(x = x, ID = sim$Id, time = sim$Start, time2 = sim$Stop, event = sim$Event, penalty = "overlapping", lambda = lam.seq, group = pars.overlapping$groups, group_variable = pars.overlapping$groups_var, penalty_weights = pars.overlapping$group_weights, tol = 1e-04, maxit = 1000, verbose = FALSE)
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [4s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(sox)
Loading required package: survival
Loading required package: glmnet
Loading required package: Matrix
Loaded glmnet 4.1-8
>
> test_check("sox")
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: coxph.wtest(fit$var[nabeta, nabeta], temp, control$toler.chol)
2: coxph(Surv(Start, Stop, Event) ~ x, init = beta, control = list(iter.max = 0, timefix = FALSE))
3: (function (beta, x, n, Start, Stop, Event) { fit.cox <- coxph(Surv(Start, Stop, Event) ~ x, init = beta, control = list(iter.max = 0, timefix = FALSE)) l <- -fit.cox$loglik[1]/n ld <- -fit.cox$first/n return(c(l, ld))})(c(0, 0, 0, 0, 0, 0, 0, 0, 0), c(1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 0, 1, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 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4: sox_cpp(x = x, start = time, stop = time2, event = event, n_unique = n, regul = regul, lam = lambdas, grp = group, grpV = group_variable, own_var = own_variable, N_own_var = no_own_variable, etaG = penalty_weights, init = par_init, l_ld = l_ld, init_stepsize = stepsize_init, ls_shrink = stepsize_shrink, partol = tol, maxit = maxit, verbose = verbose)
5: sox(x = x, ID = sim$Id, time = sim$Start, time2 = sim$Stop, event = sim$Event, penalty = "overlapping", lambda = lam.seq, group = pars.overlapping$groups, group_variable = pars.overlapping$groups_var, penalty_weights = pars.overlapping$group_weights, tol = 1e-04, maxit = 1000, verbose = FALSE)
6: eval(code, test_env)
7: eval(code, test_env)
8: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
16: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
17: source_file(path, env = env(env), desc = desc, error_call = error_call)
18: FUN(X[[i]], ...)
19: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
20: doTryCatch(return(expr), name, parentenv, handler)
21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: tryCatchList(expr, classes, parentenv, handlers)
23: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
24: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
25: 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)
26: 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)
27: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
28: test_check("sox")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-gcc