CRAN Package Check Results for Package ctsem

Last updated on 2018-05-27 19:49:18 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.5.0 19.79 1160.99 1180.78 WARN
r-devel-linux-x86_64-debian-gcc 2.5.0 17.06 867.56 884.62 WARN
r-devel-linux-x86_64-fedora-clang 2.5.0 1467.24 WARN
r-devel-linux-x86_64-fedora-gcc 2.5.0 1427.72 WARN
r-devel-windows-ix86+x86_64 2.5.0 25.00 206.00 231.00 WARN --no-vignettes
r-patched-linux-x86_64 2.5.0 14.84 1098.96 1113.80 WARN
r-patched-solaris-x86 2.5.0 256.50 ERROR
r-release-linux-x86_64 2.5.0 16.38 1103.91 1120.29 WARN
r-release-windows-ix86+x86_64 2.5.0 35.00 139.00 174.00 WARN --no-vignettes
r-release-osx-x86_64 2.5.0 WARN
r-oldrel-windows-ix86+x86_64 2.5.0 19.00 152.00 171.00 OK --no-vignettes
r-oldrel-osx-x86_64 2.5.0 WARN

Check Details

Version: 2.5.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ctsem.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.5.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ctsem.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 2.5.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/data/gannet/ripley/R/packages/tests-clang/ctsem.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 2.5.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/data/gannet/ripley/R/packages/tests-devel/ctsem.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 2.5.0
Flags: --no-vignettes
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See 'd:/Rcompile/CRANpkg/local/3.6/ctsem.Rcheck/00install.out' for details.
    Information on the location(s) of code generating the 'Note's can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to 'yes'.
Flavor: r-devel-windows-ix86+x86_64

Version: 2.5.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ctsem.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-patched-linux-x86_64

Version: 2.5.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/ripley/R/packages/tests32/ctsem.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-patched-solaris-x86

Version: 2.5.0
Check: examples
Result: ERROR
    Running examples in ‘ctsem-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))
    > AnomAuthfit <- ctFit(AnomAuth, AnomAuthmodel)
    Running ctsemCarefulFit with 14 parameters
    
    Begin fit attempt 1 of at maximum 16 tries
    
     *** caught segfault ***
    address 8, cause 'memory not mapped'
    
    Traceback:
     1: runHelper(model, frontendStart, intervals, silent, suppressWarnings, unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer)
     2: mxRun(model, suppressWarnings = T, unsafe = T, silent = T, intervals = FALSE)
     3: doTryCatch(return(expr), name, parentenv, handler)
     4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     5: tryCatchList(expr, classes, parentenv, handlers)
     6: 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))})
     7: try(mxRun(model, suppressWarnings = T, unsafe = T, silent = T, intervals = FALSE))
     8: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
     9: suppressWarnings(try(mxRun(model, suppressWarnings = T, unsafe = T, silent = T, intervals = FALSE)))
    10: 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)
    11: ctFit(AnomAuth, AnomAuthmodel)
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 2.5.0
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    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
    Running ctsemCarefulFit with 16 parameters
    
    Begin fit attempt 1 of at maximum 16 tries
    Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings, :
     Attempted to set row and column (1, 1) in algebra "ctsem.discreteDRIFT_i3 arg 0" with dimensions 0 x 0.
    
     Fit attempt generated errors
    
    Begin fit attempt 2 of at maximum 16 tries
    
     Lowest minimum so far: 16731.2801022022
    Error in eigen(fit$output$calculatedHessian, symmetric = T, only.values = T) :
     infinite or missing values in 'x'
    
     Eigenvalues of Hessian could not be calculated
    
    Begin fit attempt 3 of at maximum 16 tries
    
     Lowest minimum so far: 4718.41277567749
    
     Not all eigenvalues of Hessian are greater than 0: 9492.6814078849, 2374.23607825735, 1097.2613337692, 311.671931569775, 249.789995016178, 196.824329721417, 114.712595503086, 36.7094394559325, 21.1894280261706, 0.00127331849772145, 0.000804907577667918, 0.000000305923479119676, 1.95617772710243e-21, -2.26727773099804e-19, -0.00000000000000210601109606258, -0.0000000819190355577517
    
    Begin fit attempt 4 of at maximum 16 tries
    
     Lowest minimum so far: 4718.15674883507
    
     Not all eigenvalues of Hessian are greater than 0: 9275.91109540151, 2380.96508490923, 1032.18840139609, 302.677713400055, 258.803538676843, 175.729678372449, 109.867330439412, 43.0898016649808, 21.5418844546363, 0.000925312164676242, 0.0000307610761771875, 0.0000016753864723605, 2.4804114889388e-23, -1.39791775925758e-20, -0.0000000000000433138078741889, -0.00000119095617290891
    
    Begin fit attempt 5 of at maximum 16 tries
    
     Fit attempt worse than current best: 4866.23323112589 vs 4718.15674883507
    
    Begin fit attempt 6 of at maximum 16 tries
    
     Fit attempt generated errors
    
    Begin fit attempt 7 of at maximum 16 tries
    
     Lowest minimum so far: 4718.14061494089
    
    Solution found
    
    Running ctsemCarefulFit with 15 parameters
    
    Begin fit attempt 1 of at maximum 16 tries
    
     Lowest minimum so far: 4196.73541494076
    
    Solution found
    
    NPSOL optimizer not available - switching to CSOLNP - consider installing OpenMx using command: source('http://openmx.psyc.virginia.edu/getOpenMx.R')
    Running ctsem with 16 parameters
    
     *** caught segfault ***
    address fa120350, cause 'memory not mapped'
    
    Traceback:
     1: runHelper(model, frontendStart, intervals, silent, suppressWarnings, unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer)
     2: mxRun(ctfitobj$mxobj, intervals = TRUE)
     3: ctCI(example1fit, confidenceintervals = "DRIFT")
     4: eval(expr, envir, enclos)
     5: eval(expr, envir, enclos)
     6: withVisible(eval(expr, envir, enclos))
     7: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
     8: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
     9: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    10: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
    11: evaluate::evaluate(...)
    12: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))
    13: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)))
    14: block_exec(params)
    15: call_block(x)
    16: process_group.block(group)
    17: process_group(group)
    18: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
    19: process_file(text, output)
    20: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv())
    21: engine$weave(file, quiet = quiet, encoding = enc)
    22: doTryCatch(return(expr), name, parentenv, handler)
    23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    24: tryCatchList(expr, classes, parentenv, handlers)
    25: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) find_vignette_product(name, by = "weave", engine = engine)}, error = function(e) { stop(gettextf("processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)), domain = NA, call. = FALSE)})
    26: buildVignettes(dir = "/home/ripley/R/packages/tests32/ctsem.Rcheck/vign_test/ctsem")
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 2.5.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ctsem.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-release-linux-x86_64

Version: 2.5.0
Flags: --no-vignettes
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See 'd:/Rcompile/CRANpkg/local/3.5/ctsem.Rcheck/00install.out' for details.
    Information on the location(s) of code generating the 'Note's can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to 'yes'.
Flavor: r-release-windows-ix86+x86_64

Version: 2.5.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ctsem.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-release-osx-x86_64

Version: 2.5.0
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    
    Begin fit attempt 2 of at maximum 16 tries
    
     Lowest minimum so far: 4203.31303320986
    
    Solution found
    
    NPSOL optimizer not available - switching to CSOLNP - consider installing OpenMx using command: source('http://openmx.psyc.virginia.edu/getOpenMx.R')
    Running ctsem with 19 parameters
    Unique discreteDRIFT calculations per step required = 5
    Unique discreteCINT calculations per step required = 5
    Unique discreteDIFFUSION calculations per step required = 5
    2 / 2 latent variables required for covariance calculations
    Compiling model, ignore forthcoming warning re number of chains...
    the number of chains is less than 1; sampling not done
    Sampling...
    error occurred during calling the sampler; sampling not done
    error occurred during calling the sampler; sampling not done
    Warning in .local(object, ...) :
     some chains had errors; consider specifying chains = 1 to debug
    here are whatever error messages were returned
    Quitting from lines 294-295 (hierarchical.rnw)
    Error: processing vignette 'hierarchical.rnw' failed with diagnostics:
    argument is of length zero
    Execution halted
Flavor: r-release-osx-x86_64

Version: 2.5.0
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    
     Lowest minimum so far: 4203.3130332814
    
    Solution found
    
    NPSOL optimizer not available - switching to CSOLNP - consider installing OpenMx using command: source('http://openmx.psyc.virginia.edu/getOpenMx.R')
    Running ctsem with 19 parameters
    Warning in has_utility("pdfcrop") :
     pdfcrop not installed or not in PATH
    Unique discreteDRIFT calculations per step required = 5
    Unique discreteCINT calculations per step required = 5
    Unique discreteDIFFUSION calculations per step required = 5
    2 / 2 latent variables required for covariance calculations
    Compiling model, ignore forthcoming warning re number of chains...
    the number of chains is less than 1; sampling not done
    Sampling...
    error occurred during calling the sampler; sampling not done
    error occurred during calling the sampler; sampling not done
    Warning in .local(object, ...) :
     some chains had errors; consider specifying chains = 1 to debug
    here are whatever error messages were returned
    Quitting from lines 294-295 (hierarchical.rnw)
    Error: processing vignette 'hierarchical.rnw' failed with diagnostics:
    argument is of length zero
    Execution halted
Flavor: r-oldrel-osx-x86_64