CRAN Package Check Results for Package ctsemOMX

Last updated on 2020-12-04 00:48:19 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.2 22.32 648.56 670.88 OK
r-devel-linux-x86_64-debian-gcc 1.0.2 20.74 445.08 465.82 OK
r-devel-linux-x86_64-fedora-clang 1.0.2 769.70 OK
r-devel-linux-x86_64-fedora-gcc 1.0.2 739.86 OK
r-devel-windows-ix86+x86_64 1.0.2 48.00 176.00 224.00 OK --no-vignettes
r-patched-linux-x86_64 1.0.2 12.97 586.41 599.38 OK
r-patched-solaris-x86 1.0.2 344.80 ERROR
r-release-linux-x86_64 1.0.2 12.95 587.71 600.66 OK
r-release-macos-x86_64 1.0.2 OK
r-release-windows-ix86+x86_64 1.0.2 37.00 267.00 304.00 OK --no-vignettes
r-oldrel-macos-x86_64 1.0.2 OK
r-oldrel-windows-ix86+x86_64 1.0.2 44.00 231.00 275.00 OK --no-vignettes

Check Details

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
    
     *** caught segfault ***
    address 1cc60ee5, cause 'memory not mapped'
    
     *** caught segfault ***
    address 1cc60ee5, cause 'memory not mapped'
    
    Traceback:
     1: runHelper(model, frontendStart, intervals, silent, suppressWarnings, unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer, beginMessage)
     2: OpenMx::mxRun(model)
     3: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
     4: suppressWarnings(OpenMx::mxRun(model))
     5: doTryCatch(return(expr), name, parentenv, handler)
     6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     7: tryCatchList(expr, classes, parentenv, handlers)
     8: 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")conditionMessage.simpleError 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))})
     9: try(suppressWarnings(OpenMx::mxRun(model)))
    10: carefulFit(model, traitExtension = traitExtension, manifestTraitvarExtension = manifestTraitvarExtension, weighting = carefulFitWeight)
    11: ctFit(AnomAuth, AnomAuthmodel)
    An irrecoverable exception occurred. R is aborting now ...
    Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings, :
     promise already under evaluation: recursive default argument reference or earlier problems?
    Error in lapply(names(model@matrices), getParametersHelper, model, free, :
     trying to get slot "matrices" from an object (class "try-error") that is not an S4 object
Flavor: r-patched-solaris-x86

Version: 1.0.2
Check: tests
Result: ERROR
     Running ‘testthat.R’ [23s/63s]
    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")
    
     *** caught segfault ***
     address 8, 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(), reporter = reporter)
     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$estimate[-1], tolerance = 0.001)})
     25: eval(code, test_env)
     26: eval(code, test_env)
     27: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
     28: doTryCatch(return(expr), name, parentenv, handler)
     29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     30: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     31: doTryCatch(return(expr), name, parentenv, handler)
     32: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     33: tryCatchList(expr, classes, parentenv, handlers)
     34: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
     35: test_code(NULL, exprs, env)
     36: source_file(path, child_env(env), wrap = wrap)
     37: FUN(X[[i]], ...)
     38: lapply(test_paths, test_one_file, env = env, wrap = wrap)
     39: force(code)
     40: doWithOneRestart(return(expr), restart)
     41: withOneRestart(expr, restarts[[1L]])
     42: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     43: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, wrap = wrap))
     44: test_files(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, wrap = wrap, load_package = load_package)
     45: 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, wrap = wrap, load_package = load_package, parallel = parallel)
     46: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
     47: 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 252dacc0, cause 'memory not mapped'
Flavor: r-patched-solaris-x86