Last updated on 2020-08-07 01:50:17 CEST.
| Package | ERROR | WARN | NOTE | OK |
|---|---|---|---|---|
| ctsem | 3 | 1 | 8 | |
| ctsemOMX | 4 | 8 |
Current CRAN status: ERROR: 3, WARN: 1, NOTE: 8
Version: 3.3.8
Flags: --no-vignettes
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavors: r-devel-linux-x86_64-debian-clang, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 3.3.8
Flags: --no-vignettes
Check: for GNU extensions in Makefiles
Result: NOTE
GNU make is a SystemRequirements.
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64
Version: 3.3.8
Check: installed package size
Result: NOTE
installed size is 136.9Mb
sub-directories of 1Mb or more:
R 1.1Mb
data 1.4Mb
doc 1.0Mb
libs 133.2Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-patched-solaris-x86, r-release-macos-x86_64, r-oldrel-macos-x86_64
Version: 3.3.8
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘pkgbuild’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-macos-x86_64, r-oldrel-macos-x86_64
Version: 3.3.8
Check: for GNU extensions in Makefiles
Result: NOTE
GNU make is a SystemRequirements.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-macos-x86_64, r-oldrel-macos-x86_64
Version: 3.3.8
Check: for detritus in the temp directory
Result: NOTE
Found the following files/directories:
‘par-7269706c6579’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 3.3.8
Flags: --no-vignettes
Check: installed package size
Result: NOTE
installed size is 8.5Mb
sub-directories of 1Mb or more:
R 1.1Mb
data 1.4Mb
doc 1.0Mb
libs 4.8Mb
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64
Version: 3.3.8
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘hierarchicalmanual.rnw’ using knitr
System dimensions inferred from LAMBDA
n.TDpred inferred inferred from TDpredNames
n.TIpred inferred inferred from TIpredNames
Custom par cint2 set as: param = cint2; transform = 10 * param; indvarying = TRUE; sdscale = 1; cint2 tipred effects from: TI1
System dimensions inferred from manifestNames and latentNames
n.TDpred inferred inferred from TDpredNames
n.TIpred inferred inferred from TIpredNames
LAMBDA vector spec input rowwise into 2 * 2 matrix:
MANIFESTMEANS specified via single value -- filling 2 * 1 matrix:
CINT vector spec input rowwise into 2 * 1 matrix:
Custom par cint2 set as: param = cint2; transform = 10 * param; indvarying = TRUE; sdscale = 1; cint2 tipred effects from: TI1
Free T0VAR parameters as well as indvarying T0MEANS -- fixing T0VAR pars to diag matrix of 1e-3
Free T0VAR parameters as well as indvarying T0MEANS -- fixing T0VAR pars to diag matrix of 1e-3
Maximum likelihood estimation requested
Missingness in TIpreds - single imputing 1 NA's to allow optimization -- TI predictor effect estimates will be overly confident.
Missingness in TDpreds! Replaced by zeroes...
Using 2/16 logical CPU cores
Doing 1st pass with priors on reduced data set
Optimizing...
Including TI predictors...
Estimating Hessian
Computing quantities for 1000 samples...
Computing state estimates..
Computing quantities for 1 samples...
Computing temporal regression coefficients for 500 samples, may take a moment...
Maximum a posteriori estimation requested
Using 2/16 logical CPU cores
Optimizing...
Estimating Hessian
Computing quantities for 10000 samples...
Computing state estimates..
Computing quantities for 1 samples...
Computing state estimates..
Computing quantities for 1 samples...
Getting 100 samples by 20 subjects for 2000 total samples
Calculating time independent predictor effects...
Free T0VAR parameters as well as indvarying T0MEANS -- fixing T0VAR pars to diag matrix of 1e-3
Free T0VAR parameters as well as indvarying T0MEANS -- fixing T0VAR pars to diag matrix of 1e-3
Free T0VAR parameters as well as indvarying T0MEANS -- fixing T0VAR pars to diag matrix of 1e-3
Free T0VAR parameters as well as indvarying T0MEANS -- fixing T0VAR pars to diag matrix of 1e-3
Custom par ma1 set as: param = ma1; transform = log(1+(exp(param))); indvarying = FALSE; sdscale = 1;
Custom par a21 set as: param = a21; transform = -log(1+exp(param)); indvarying = FALSE; sdscale = 1;
Custom par m1 set as: param = m1; transform = param*10+44; indvarying = TRUE; sdscale = 1;
Setting DRIFT diagonals of 0 to approximate 0 of -0.000001
Bayesian estimation via Stan's NUTS sampler requested
Individual variation not possible as only 1 subject! indvarying set to FALSE on all parameters
Free T0VAR parameters fixed to diagonal matrix of 1 as only 1 subject - consider appropriateness!
Sampling...
Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#bulk-ess
Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#tail-ess
Computing state estimates..
Computing quantities for 1 samples...
Error: processing vignette 'hierarchicalmanual.rnw' failed with diagnostics:
Running 'texi2dvi' on 'hierarchicalmanual.tex' failed.
Messages:
/usr/local/bin/texi2dvi: line 365: 13668 Killed "$@" 2>&5 1>&2
/usr/local/bin/texi2dvi: biber failed
--- failed re-building ‘hierarchicalmanual.rnw’
SUMMARY: processing the following file failed:
‘hierarchicalmanual.rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-solaris-x86
Current CRAN status: ERROR: 4, OK: 8
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