CRAN Package Check Results for Package sox

Last updated on 2024-10-14 09:49:19 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2 27.45 86.83 114.28 OK
r-devel-linux-x86_64-debian-gcc 1.2 23.12 58.59 81.71 OK
r-devel-linux-x86_64-fedora-clang 1.2 202.68 OK
r-devel-linux-x86_64-fedora-gcc 1.2 158.28 ERROR
r-devel-windows-x86_64 1.2 39.00 118.00 157.00 OK
r-patched-linux-x86_64 1.2 31.13 80.09 111.22 OK
r-release-linux-x86_64 1.2 33.59 80.49 114.08 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 38.00 115.00 153.00 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 45.00 147.00 192.00 OK

Check Details

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, 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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) 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, 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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