Last updated on 2020-08-07 01:49:40 CEST.
Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
---|---|---|---|---|---|---|
r-devel-linux-x86_64-debian-clang | 1.0.2 | 0.70 | 2.69 | 3.39 | ERROR | |
r-devel-linux-x86_64-debian-gcc | 1.0.2 | 18.79 | 445.44 | 464.23 | OK | |
r-devel-linux-x86_64-fedora-clang | 1.0.2 | 736.19 | OK | |||
r-devel-linux-x86_64-fedora-gcc | 1.0.2 | 719.80 | OK | |||
r-devel-windows-ix86+x86_64 | 1.0.2 | 62.00 | 223.00 | 285.00 | OK | --no-vignettes |
r-patched-linux-x86_64 | 1.0.2 | 0.35 | 2.63 | 2.98 | ERROR | |
r-patched-solaris-x86 | 1.0.2 | 305.60 | ERROR | |||
r-release-linux-x86_64 | 1.0.2 | 0.60 | 2.66 | 3.26 | ERROR | |
r-release-macos-x86_64 | 1.0.2 | OK | ||||
r-release-windows-ix86+x86_64 | 1.0.2 | 43.00 | 267.00 | 310.00 | OK | --no-vignettes |
r-oldrel-macos-x86_64 | 1.0.2 | OK | ||||
r-oldrel-windows-ix86+x86_64 | 1.0.2 | 41.00 | 256.00 | 297.00 | OK | --no-vignettes |
Version: 1.0.2
Check: package dependencies
Result: ERROR
Package required but not available: 'ctsem'
See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.0.2
Check: examples
Result: ERROR
Running examples in ‘ctsemOMX-Ex.R’ failed
The error most likely occurred in:
> ### Name: ctGenerateFromFit
> ### Title: Generates data according to the model estimated in a ctsemFit
> ### object.
> ### Aliases: ctGenerateFromFit
>
> ### ** Examples
>
>
> data(AnomAuth)
> AnomAuthmodel <- ctModel(LAMBDA = matrix(c(1, 0, 0, 1), nrow = 2, ncol = 2),
+ Tpoints = 5, n.latent = 2, n.manifest = 2, MANIFESTVAR=diag(0, 2))
Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
> AnomAuthfit <- ctFit(AnomAuth, AnomAuthmodel)
wide format data detected
Running ctsemCarefulFit with 14 parameters
Running ctsem with 14 parameters
Beginning initial fit attempt
Running ctsem with 14 parameters
*** caught segfault ***
address 6ccb7930, cause 'memory not mapped'
Traceback:
1: runHelper(model, frontendStart, intervals, silent, suppressWarnings, unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer, beginMessage)
2: mxRun(model = model, suppressWarnings = T, unsafe = T, silent = T, intervals = intervals, beginMessage = T)
3: runWithCounter(model, numdone, silent, intervals = F)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(runWithCounter(model, numdone, silent, intervals = F))
9: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
10: suppressWarnings(try(runWithCounter(model, numdone, silent, intervals = F)))
11: mxTryHard(model, initialTolerance = 1e-14, initialGradientIterations = 1, showInits = showInits, checkHess = TRUE, greenOK = FALSE, iterationSummary = iterationSummary, bestInitsOutput = FALSE, verbose = verbose, extraTries = retryattempts, loc = 0.5, scale = 0.2, paste = FALSE)
12: ctFit(AnomAuth, AnomAuthmodel)
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86
Version: 1.0.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [26s/60s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ctsemOMX)
Loading required package: ctsem
Loading required package: Rcpp
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX')
Loading required package: OpenMx
To take full advantage of multiple cores, use:
mxOption(key='Number of Threads', value=parallel::detectCores()) #now
Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx)
Attaching package: 'ctsemOMX'
The following objects are masked from 'package:ctsem':
ctFit, ctIndplot
> pdf(NULL)
> test_check("ctsemOMX")
Error: C stack usage 333747348 is too close to the limit
Error: C stack usage 333747348 is too close to the limit
*** caught segfault ***
address 0, cause 'memory not mapped'
Traceback:
1: runHelper(model, frontendStart, intervals, silent, suppressWarnings, unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer, beginMessage)
2: mxRun(model = model, suppressWarnings = T, unsafe = T, silent = T, intervals = intervals, beginMessage = T)
3: runWithCounter(model, numdone, silent, intervals = F)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(runWithCounter(model, numdone, silent, intervals = F))
9: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
10: suppressWarnings(try(runWithCounter(model, numdone, silent, intervals = F)))
11: mxTryHard(fit$mxobj, initialTolerance = 1e-14, initialGradientIterations = 1, showInits = FALSE, checkHess = TRUE, greenOK = FALSE, iterationSummary = FALSE, bestInitsOutput = FALSE, verbose = fit$ctfitargs$verbose, extraTries = fit$ctfitargs$retryattempts, loc = 1, scale = 0.1, paste = FALSE)
12: ctRefineTo(dat = gd, m, retryattempts = 3, objective = "Kalman", stationary = c("T0MEANS", "T0VAR"), carefulFit = TRUE)
13: eval(code, test_env)
14: eval(code, test_env)
15: 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)
16: doTryCatch(return(expr), name, parentenv, handler)
17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
18: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
21: tryCatchList(expr, classes, parentenv, handlers)
22: 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) { })
23: test_code(desc, code, env = parent.frame())
24: test_that("time calc", { set.seed(4) nsubjects = 20 TDPREDEFFECT = matrix(c(-20, 1, -1, 20), 2, 2) gm = ctModel(Tpoints = 10, n.latent = 2, n.manifest = 3, LAMBDA = matrix(c(1, 0, 0, 0, 1, 0.5), ncol = 2), DRIFT = matrix(c(-0.3, 0, 0, -0.05), 2, 2), DIFFUSION = diag(2, 2), CINT = matrix(c(5, 3), ncol = 1), TDPREDEFFECT = TDPREDEFFECT, TDPREDVAR = diag(0.002, 10 * 2), MANIFESTVAR = diag(0.3, 3), T0VAR = diag(2), n.TDpred = 2, TDPREDMEANS = matrix(rep(c(1, rep(0, 4), 0, rep(0, 4)), 2), ncol = 1)) gd = ctGenerate(gm, nsubjects, burnin = 50) m = ctModel(Tpoints = 10, n.latent = 2, n.manifest = 3, LAMBDA = matrix(c(1, 0, 0, 0, 1, 0.5), ncol = 2), DRIFT = matrix(c(-0.3, 0, 0, -0.05), 2, 2), TDPREDEFFECT = matrix(c("td1", 1, -1, 20), 2, 2), CINT = matrix(c(5, 3), ncol = 1), MANIFESTMEANS = matrix(c(0, 0, 0), ncol = 1), n.TDpred = 2) f1 = ctRefineTo(dat = gd, m, retryattempts = 3, objective = "Kalman", stationary = c("T0MEANS", "T0VAR"), carefulFit = TRUE) f2 = ctRefineTo(dat = gd, m, retryattempts = 3, objective = "mxRAM", stationary = c("T0MEANS", "T0VAR"), carefulFit = TRUE) expect_equal(f1$mxobj$output$estimate[-1], f2$mxobj$output$estimate[-1], tolerance = 0.001)})
25: eval(code, test_env)
26: eval(code, test_env)
27: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
31: doTryCatch(return(expr), name, parentenv, handler)
32: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
33: tryCatchList(expr, classes, parentenv, handlers)
34: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
35: test_code(NULL, exprs, env)
36: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
37: force(code)
38: doWithOneRestart(return(expr), restart)
39: withOneRestart(expr, restarts[[1L]])
40: withRestarts(testthat_abort_reporter = function() NULL, force(code))
41: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter, { reporter$start_file(basename(path)) lister$start_file(basename(path)) source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap) reporter$.end_context() reporter$end_file() })
42: FUN(X[[i]], ...)
43: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
44: force(code)
45: doWithOneRestart(return(expr), restart)
46: withOneRestart(expr, restarts[[1L]])
47: withRestarts(testthat_abort_reporter = function() NULL, force(code))
48: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap))
49: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
50: 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)
51: 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)
52: test_check("ctsemOMX")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86
Version: 1.0.2
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘ctsem.rnw’ using knitr
Observations with missing time information found - removing 1 rows
Discrete time points created: 4
Extracting first non-missing value for time independent predictors
imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
wide format data detected
Running ctsemCarefulFit with 16 parameters
*** caught segfault ***
address 20, cause 'memory not mapped'
*** caught segfault ***
address 4505d030, cause 'memory not mapped'
Warning: stack imbalance in '-', 68 then 69
Quitting from lines 410-415 (ctsem.rnw)
Flavor: r-patched-solaris-x86