Last updated on 2024-11-13 09:49:40 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2 | 24.40 | 87.15 | 111.55 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.2 | 23.12 | 60.20 | 83.32 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.2 | 186.99 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2 | 153.97 | ERROR | |||
| r-devel-windows-x86_64 | 1.2 | 35.00 | 113.00 | 148.00 | OK | |
| r-patched-linux-x86_64 | 1.2 | 31.19 | 80.62 | 111.81 | OK | |
| r-release-linux-x86_64 | 1.2 | 30.94 | 81.20 | 112.14 | OK | |
| r-release-macos-arm64 | 1.2 | 67.00 | OK | |||
| r-release-macos-x86_64 | 1.2 | 128.00 | OK | |||
| r-release-windows-x86_64 | 1.2 | 36.00 | 120.00 | 156.00 | OK | |
| r-oldrel-macos-arm64 | 1.2 | 58.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.2 | 101.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.2 | 44.00 | 147.00 | 191.00 | OK |
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’
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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2.11979950396975, -1.60282891480486, -1.60282891480486, 1.59288254302394, 0.909668234529367, 0.909668234529367, -1.64943177911453, -1.64943177911453, -1.64943177911453, -0.436714926676307, -0.436714926676307, -0.73708792176996, -0.73708792176996, -0.885831850370681, -0.885831850370681, -0.885831850370681, -0.885831850370681, -0.885831850370681, -1.15782511798174, 0.402397088873237, 0.157818428234532, 0.157818428234532, 1.44540365574097, -0.0315375204875326, -0.0315375204875326, -0.0315375204875326, -0.0315375204875326, -0.903843820576606, -0.903843820576606, -0.903843820576606, -0.480901430934696, -0.480901430934696, -1.31433467072547, -1.31433467072547, -1.31433467072547, -1.31433467072547, -1.31433467072547, -0.61868666748541, -0.61868666748541, -0.61868666748541, -0.265300014843201, -0.265300014843201, -0.265300014843201, -1.12486337908738, -1.12486337908738, -1.12486337908738, -1.12486337908738, -1.12486337908738, 1.5211442011399, 1.5211442011399, 2.25545543939827, 0.553656234844648, 1.88016351926948, -0.328880641077259, -0.328880641077259, -0.328880641077259, -1.26767520483124, -1.26767520483124, -1.26767520483124, 0.895520070745094, 0.969723494426376, 0.65804826796191, 0.167109046845867, 0.167109046845867, 0.167109046845867, 0.0952254311102382, 0.0952254311102382, 0.0952254311102382, 0.0952254311102382, 0.686755211039724, 0.686755211039724, 0.686755211039724, 1.73292488126815, 1.73292488126815, -0.669705813597861, -0.669705813597861, 2.11317906364535, -0.035176070898106, 1.10926114597935, 1.10926114597935, -0.058937177197228, -0.058937177197228, 1.05079808384824, 1.05079808384824, -1.37415096042926, 0.106796411854337, 0.106796411854337, 0.106796411854337, 1.38861038888446, 0.793578443137482, 0.793578443137482, 0.793578443137482, -0.722018112912622, -0.722018112912622, -0.722018112912622, -0.722018112912622, 0.333777904118776, 0, 0, 0, 0, 0, 1.08382646411334, 0, 0, 0, 0, 0, -0.324368555889368, -0.324368555889368, -0.324368555889368, -0.324368555889368, 0, 0, 0, 0, 0.909668234529367, 0.909668234529367, 0, 0, 0, 0, 0, -0.73708792176996, -0.73708792176996, 0, 0, 0, 0, 0, -1.15782511798174, 0.402397088873237, 0.157818428234532, 0.157818428234532, 1.44540365574097, -0.0315375204875326, -0.0315375204875326, -0.0315375204875326, -0.0315375204875326, -0.903843820576606, -0.903843820576606, -0.903843820576606, 0, 0, -1.31433467072547, -1.31433467072547, -1.31433467072547, -1.31433467072547, -1.31433467072547, 0, 0, 0, -0.265300014843201, -0.265300014843201, -0.265300014843201, -1.12486337908738, -1.12486337908738, -1.12486337908738, -1.12486337908738, -1.12486337908738, 0, 0, 2.25545543939827, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.969723494426376, 0, 0.167109046845867, 0.167109046845867, 0.167109046845867, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2.11317906364535, 0, 1.10926114597935, 1.10926114597935, -0.058937177197228, -0.058937177197228, 0, 0, -1.37415096042926, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -0.632859527851237, -0.632859527851237, 0.576683463098741, 0.537536735428052, 0.537536735428052, 0, 0, 0, 0, 0, -1.60282891480486, -1.60282891480486, 0, 0, 0, -1.64943177911453, -1.64943177911453, -1.64943177911453, -0.436714926676307, -0.436714926676307, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -0.480901430934696, -0.480901430934696, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1.88016351926948, 0, 0, 0, -1.26767520483124, -1.26767520483124, -1.26767520483124, 0.895520070745094, 0, 0.65804826796191, 0, 0, 0, 0.0952254311102382, 0.0952254311102382, 0.0952254311102382, 0.0952254311102382, 0, 0, 0, 0, 0, 0, 0, 0, -0.035176070898106, 0, 0, 0, 0, 1.05079808384824, 1.05079808384824, 0, 0.106796411854337, 0.106796411854337, 0.106796411854337, 1.38861038888446, 0, 0, 0, -0.722018112912622, -0.722018112912622, -0.722018112912622, -0.722018112912622, 0.333777904118776, 0, 0, 0, 0, 0, 1.08382646411334, 0, 0, 0, 0.537536735428052, 0.537536735428052, -0.324368555889368, -0.324368555889368, -0.324368555889368, -0.324368555889368, 0, -1.60282891480486, -1.60282891480486, 1.59288254302394, 0.909668234529367, 0.909668234529367, -1.64943177911453, -1.64943177911453, -1.64943177911453, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.157818428234532, 0.157818428234532, 1.44540365574097, 0, 0, 0, 0, -0.903843820576606, -0.903843820576606, -0.903843820576606, 0, 0, -1.31433467072547, -1.31433467072547, -1.31433467072547, -1.31433467072547, -1.31433467072547, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1.5211442011399, 1.5211442011399, 2.25545543939827, 0, 0, -0.328880641077259, -0.328880641077259, -0.328880641077259, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.106796411854337, 0.106796411854337, 0.106796411854337, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.0502137227522389, 0.0502137227522389, 0.0502137227522389, 0.0502137227522389, 0.0502137227522389, 0, -0.632859527851237, -0.632859527851237, 0.576683463098741, 0, 0, 0, 0, 0, 0, 2.11979950396975, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -0.73708792176996, -0.73708792176996, 0, 0, 0, 0, 0, -1.15782511798174, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1.12486337908738, -1.12486337908738, -1.12486337908738, -1.12486337908738, -1.12486337908738, 0, 0, 0, 0, 0, 0, 0, 0, -1.26767520483124, -1.26767520483124, -1.26767520483124, 0.895520070745094, 0.969723494426376, 0, 0.167109046845867, 0.167109046845867, 0.167109046845867, 0.0952254311102382, 0.0952254311102382, 0.0952254311102382, 0.0952254311102382, 0.686755211039724, 0.686755211039724, 0.686755211039724, 0, 0, -0.669705813597861, -0.669705813597861, 0, -0.035176070898106, 1.10926114597935, 1.10926114597935, -0.058937177197228, -0.058937177197228, 1.05079808384824, 1.05079808384824, -1.37415096042926, 0, 0, 0, 0, 0.793578443137482, 0.793578443137482, 0.793578443137482), 50L, c(0, 1, 2, 3, 0, 0, 1, 2, 3, 4, 0, 0, 1, 0, 0, 1, 0, 1, 2, 3, 0, 0, 1, 0, 0, 1, 0, 1, 2, 0, 1, 0, 1, 0, 1, 2, 3, 4, 0, 0, 0, 1, 0, 0, 1, 2, 3, 0, 1, 2, 0, 1, 0, 1, 2, 3, 4, 0, 1, 2, 0, 1, 2, 0, 1, 2, 3, 4, 0, 1, 0, 0, 0, 0, 1, 2, 0, 1, 2, 0, 0, 0, 0, 1, 2, 0, 1, 2, 3, 0, 1, 2, 0, 1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 1, 2, 0, 0, 1, 2), c(1, 2, 3, 4, 1, 1, 2, 3, 4, 5, 1, 1, 2, 1, 1, 2, 1, 2, 3, 4, 1, 1, 2, 1, 1, 2, 1, 2, 3, 1, 2, 1, 2, 1, 2, 3, 4, 5, 1, 1, 1, 2, 1, 1, 2, 3, 4, 1, 2, 3, 1, 2, 1, 2, 3, 4, 5, 1, 2, 3, 1, 2, 3, 1, 2, 3, 4, 5, 1, 2, 1, 1, 1, 1, 2, 3, 1, 2, 3, 1, 1, 1, 1, 2, 3, 1, 2, 3, 4, 1, 2, 3, 1, 2, 1, 2, 1, 1, 1, 2, 1, 2, 1, 2, 1, 1, 2, 3, 1, 1, 2, 3), c(0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1))
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