CRAN Package Check Results for Package ctsem

Last updated on 2016-10-25 23:47:32.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1.6 3.25 383.70 386.95 OK
r-devel-linux-x86_64-debian-gcc 1.1.6 3.43 296.11 299.54 OK
r-devel-linux-x86_64-fedora-clang 1.1.6 796.78 OK
r-devel-linux-x86_64-fedora-gcc 1.1.6 981.26 OK
r-devel-windows-ix86+x86_64 1.1.6 14.00 214.00 228.00 OK --no-vignettes
r-patched-linux-x86_64 1.1.6 3.30 286.56 289.87 OK
r-patched-solaris-sparc 1.1.6 1926.40 ERROR
r-patched-solaris-x86 1.1.6 144.90 ERROR
r-release-linux-x86_64 1.1.6 3.60 282.42 286.02 OK
r-release-osx-x86_64-mavericks 1.1.6 WARN
r-release-windows-ix86+x86_64 1.1.6 11.00 218.00 229.00 OK --no-vignettes
r-oldrel-windows-ix86+x86_64 1.1.6 16.00 219.00 235.00 OK --no-vignettes

Check Details

Version: 1.1.6
Check: tests
Result: ERROR
    Running the tests in ‘tests/dotest.R’ failed.
    Last 13 lines of output:
     23415.93 not equal to AnomAuthfit$mxobj$output$Minus2LogLikelihood.
     1/1 mismatches
     [1] 23416 - NA == NA
    
    
     2. Failure: time calc (@test-knownFits.R#48) -----------------------------------
     summ1$ctparameters[, 1:2] not equal to summ2$ctparameters[, 1:2].
     Component "Value": Mean relative difference: 0.9618599
    
    
     DONE ===========================================================================
     Error: Test failures
     Execution halted
Flavor: r-patched-solaris-sparc

Version: 1.1.6
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: 3
    Warning: measures of time dependent predictor 1 occurring at final measurement occasion removed, as they have no time to impact processes
    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
    
     *** caught segfault ***
    address 0, cause 'memory not mapped'
    Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings, :
     Requested improper value (1, 1) from (0, 1) matrix
    Warning: stack imbalance in '<-', 206 then 212
    Warning: stack imbalance in 'if', 244 then 243
    Warning: stack imbalance in '(', 247 then 248
    Error in lapply(model@matrices, getParametersHelper, model@name, free, :
     trying to get slot "matrices" from an object (class "try-error") that is not an S4 object
    Warning: stack imbalance in '<-', 212 then 213
    Warning: stack imbalance in '{', 203 then 209
    Warning: stack imbalance in 'if', 201 then 207
    
    Traceback:
     1: conditionCall(e)
     2: value[[3L]](cond)
     3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     4: tryCatchList(expr, classes, parentenv, handlers)
     5: 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 msg <- conditionMessage(e) sm <- strsplit(msg, "\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 && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
     6: try(OpenMx::omxGetParameters(mxobj))
     7: ctFit(datawide = ctExample1, ctmodelobj = example1model)
     8: eval(expr, envir, enclos)
     9: eval(expr, envir, enclos)
    10: withVisible(eval(expr, envir, enclos))
    11: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
    12: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
    13: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler)
    14: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))
    15: in_dir(opts_knit$get("root.dir") %n% input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)))
    16: block_exec(params)
    17: call_block(x)
    18: process_group.block(group)
    19: process_group(group)
    20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "")Quitting from lines 414-419 (ctsem.rnw)
     message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), Warning: stack imbalance in '{', 233 then 232
     ") ") })
    21: process_file(text, output)
    22: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", file)) knit2pdf else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv())
    23: engine$weave(file, quiet = quiet, encoding = enc)
    24: doTryCatch(return(expr), name, parentenv, handler)
    25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    26: tryCatchList(expr, classes, parentenv, handlers)
    27: 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)})
    28: buildVignettes(dir = "/home/ripley/R/packages/tests32/ctsem.Rcheck/vign_test/ctsem")
    An irrecoverable exception occurred. R is aborting now ...
    Error: processing vignette 'ctsem.rnw' failed with diagnostics:
    R_Reprotect: only 219 protected items, can't reprotect index 219
    Execution halted
Flavor: r-patched-solaris-sparc

Version: 1.1.6
Check: tests
Result: ERROR
    Running the tests in ‘tests/dotest.R’ failed.
    Last 13 lines of output:
     26: source_file(path, new.env(parent = env), chdir = TRUE)
     27: force(code)
     28: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter, { lister$start_file(basename(path)) source_file(path, new.env(parent = env), chdir = TRUE) end_context() })
     29: FUN(X[[i]], ...)
     30: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE)
     31: force(code)
     32: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE))
     33: test_files(paths, reporter = reporter, env = env, ...)
     34: test_dir(test_path, reporter = reporter, env = env, filter = filter, ...)
     35: with_top_env(env, { test_dir(test_path, reporter = reporter, env = env, filter = filter, ...)})
     36: run_tests(package, test_path, filter, reporter, ...)
     37: test_package("ctsem")
     An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 1.1.6
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: 3
    Warning: measures of time dependent predictor 1 occurring at final measurement occasion removed, as they have no time to impact processes
    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
    
     *** caught segfault ***
    address 0, cause 'memory not mapped'
    Warning: stack imbalance in 'lazyLoadDBfetch', 246 then 247
Flavor: r-patched-solaris-x86

Version: 1.1.6
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
     Running 'texi2dvi' on 'ctsem.tex' failed.
    LaTeX errors:
    ! LaTeX Error: Missing \begin{document}.
    
    See the LaTeX manual or LaTeX Companion for explanation.
    Type H <return> for immediate help.
     ...
    ! Undefined control sequence.
    l.19 ...<d1><f3>Sw<e0>^^D,<b9><ed>E^^N0<e3>m<0b>!`6^^A<e0><eb>ׯ^^[<86>^^Q<8d>Fs<b9>\<bd>
     ^<b7>,krrR<d7><f5>H$<82><8e>^^X<8d><88>^^J
    The control sequence at the end of the top line
    of your error message was never \def'ed. If you have
    ! Missing $ inserted.
    <inserted text>
     $
    l.19 ...<f3>Sw<e0>^^D,<b9><ed>E^^N0<e3>m<0b>!`6^^A<e0><eb>ׯ^^[<86>^^Q<8d>Fs<b9>\<bd>^
     <b7>,krrR<d7><f5>H$<82><8e>^^X<8d><88>^^J
    ! Please use \mathaccent for accents in math mode.
    \add@accent ...@spacefactor \spacefactor }\accent
     #1 #2\egroup \spacefactor ...
    l.21 <ec>B<bc>\.g
    
    Calls: buildVignettes -> texi2pdf -> texi2dvi
    Execution halted
Flavor: r-release-osx-x86_64-mavericks