CRAN Package Check Results for Package rstansim

Last updated on 2018-12-30 23:47:47 CET.

Check Details

Version: 0.1.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    duplicated vignette title:
     ‘Model Fitting’
    
    --- re-building ‘managing-results.Rmd’ using rmarkdown
    --- finished re-building ‘managing-results.Rmd’
    
    --- re-building ‘model-fitting.Rmd’ using rmarkdown
    --- finished re-building ‘model-fitting.Rmd’
    
    --- re-building ‘reproducability.Rmd’ using rmarkdown
    --- finished re-building ‘reproducability.Rmd’
    
    --- re-building ‘simulating_data.Rmd’ using rmarkdown
    Loading required package: Rcpp
    --- finished re-building ‘simulating_data.Rmd’
    
    --- re-building ‘using-rstansim.Rmd’ using rmarkdown
    Error in (function (x) : attempt to apply non-function
    recompiling to avoid crashing R session
    Loading required package: ggridges
    
    Attaching package: 'ggridges'
    
    The following object is masked from 'package:ggplot2':
    
     scale_discrete_manual
    
    The ggjoy package has been deprecated. Please switch over to the
    ggridges package, which provides the same functionality. Porting
    guidelines can be found here:
    https://github.com/clauswilke/ggjoy/blob/master/README.md
    Picking joint bandwidth of 0.0149
    Picking joint bandwidth of 0.0149
    Picking joint bandwidth of 0.0128
    Picking joint bandwidth of 0.0129
    Picking joint bandwidth of 0.0161
    Picking joint bandwidth of 0.0229
    --- finished re-building ‘using-rstansim.Rmd’
    
    Error: Duplicate vignette titles
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.1.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    duplicated vignette title:
     ‘Model Fitting’
    
    --- re-building ‘managing-results.Rmd’ using rmarkdown
    --- finished re-building ‘managing-results.Rmd’
    
    --- re-building ‘model-fitting.Rmd’ using rmarkdown
    --- finished re-building ‘model-fitting.Rmd’
    
    --- re-building ‘reproducability.Rmd’ using rmarkdown
    --- finished re-building ‘reproducability.Rmd’
    
    --- re-building ‘simulating_data.Rmd’ using rmarkdown
    Loading required package: Rcpp
    --- finished re-building ‘simulating_data.Rmd’
    
    --- re-building ‘using-rstansim.Rmd’ using rmarkdown
    Loading required package: Rcpp
    recompiling to avoid crashing R session
    Loading required package: ggridges
    
    Attaching package: 'ggridges'
    
    The following object is masked from 'package:ggplot2':
    
     scale_discrete_manual
    
    The ggjoy package has been deprecated. Please switch over to the
    ggridges package, which provides the same functionality. Porting
    guidelines can be found here:
    https://github.com/clauswilke/ggjoy/blob/master/README.md
    Picking joint bandwidth of 0.0149
    Picking joint bandwidth of 0.0149
    Picking joint bandwidth of 0.0128
    Picking joint bandwidth of 0.0129
    Picking joint bandwidth of 0.0161
    Picking joint bandwidth of 0.0229
    --- finished re-building ‘using-rstansim.Rmd’
    
    Error: Duplicate vignette titles.
     Ensure that the %\VignetteIndexEntry lines in the vignette sources
     correspond to the vignette titles.
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.1.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    duplicated vignette title:
     ‘Model Fitting’
    
    --- re-building ‘managing-results.Rmd’ using rmarkdown
    --- finished re-building ‘managing-results.Rmd’
    
    --- re-building ‘model-fitting.Rmd’ using rmarkdown
    --- finished re-building ‘model-fitting.Rmd’
    
    --- re-building ‘reproducability.Rmd’ using rmarkdown
    --- finished re-building ‘reproducability.Rmd’
    
    --- re-building ‘simulating_data.Rmd’ using rmarkdown
    Loading required package: Rcpp
    --- finished re-building ‘simulating_data.Rmd’
    
    --- re-building ‘using-rstansim.Rmd’ using rmarkdown
    recompiling to avoid crashing R session
    Loading required package: ggridges
    
    Attaching package: 'ggridges'
    
    The following object is masked from 'package:ggplot2':
    
     scale_discrete_manual
    
    The ggjoy package has been deprecated. Please switch over to the
    ggridges package, which provides the same functionality. Porting
    guidelines can be found here:
    https://github.com/clauswilke/ggjoy/blob/master/README.md
    Picking joint bandwidth of 0.0149
    Picking joint bandwidth of 0.0149
    Picking joint bandwidth of 0.0128
    Picking joint bandwidth of 0.0129
    Picking joint bandwidth of 0.0161
    Picking joint bandwidth of 0.0229
    --- finished re-building ‘using-rstansim.Rmd’
    
    Error: Duplicate vignette titles
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64

Version: 0.1.1
Check: tests
Result: ERROR
     Running ‘testthat.R’ [112s/133s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > Sys.setenv("R_TESTS" = "")
     > library(testthat)
     > library(rstansim)
     Loading required package: Rcpp
     >
     > test_check("rstansim")
    
     *** caught segfault ***
     address 10, cause 'memory not mapped'
    
     Traceback:
     1: FUN(X[[i]], ...)
     2: lapply(name, function(id) { v <- .Internal(getSymbolInfo(as.character(id), PACKAGE, as.logical(withRegistrationInfo))) if (is.null(v)) { msg <- paste("no such symbol", id) if (length(pkgName) && nzchar(pkgName)) msg <- paste(msg, "in package", pkgName) stop(msg, domain = NA) } names(v) <- c("name", "address", "package", "numParameters")[seq_along(v)] v})
     3: getNativeSymbolInfo(name, PACKAGE)
     4: doTryCatch(return(expr), name, parentenv, handler)
     5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     6: tryCatchList(expr, classes, parentenv, handlers)
     7: tryCatch(getNativeSymbolInfo(name, PACKAGE), error = function(e) e)
     8: Module(module, mustStart = TRUE)
     9: .getModulePointer(x)
     10: new("Module", .xData = <environment>)$stan_fit4model4f5d1777561a_simtestreg
     11: new("Module", .xData = <environment>)$stan_fit4model4f5d1777561a_simtestreg
     12: eval(call("$", mod, paste("stan_fit4", model_cppname, sep = "")))
     13: eval(call("$", mod, paste("stan_fit4", model_cppname, sep = "")))
     14: object@mk_cppmodule(object)
     15: .local(object, ...)
     16: rstan::sampling(object = cmodel, data = input_data, init = list(param_values), iter = nsim, chains = 1, cores = use_cores, warmup = 0, algorithm = "Fixed_param", seed = seed)
     17: rstan::sampling(object = cmodel, data = input_data, init = list(param_values), iter = nsim, chains = 1, cores = use_cores, warmup = 0, algorithm = "Fixed_param", seed = seed)
     18: simulate_internal(cmodel = compiled_model, input_data = input_data, vars = vars, param_values = param_values, nsim = nsim, use_cores = use_cores, sim_drop = sim_drop, seed = seed)
     19: simulate_data(file = "data-raw/simtestreg.stan", data_name = "saved stansim_data", input_data = reg_data, nsim = 1, path = "testdir", param_values = test_vals, vars = c("sim_x", "sim_y", "N"), use_cores = 1)
     20: withVisible(code)
     21: force(code)
     22: withr::with_output_sink(temp, withVisible(code))
     23: eval_with_output(code, print = print, width = width)
     24: capture_output_lines(code, print, width = width)
     25: capture_output(ss_data <- simulate_data(file = "data-raw/simtestreg.stan", data_name = "saved stansim_data", input_data = reg_data, nsim = 1, path = "testdir", param_values = test_vals, vars = c("sim_x", "sim_y", "N"), use_cores = 1))
     26: eval(code, test_env)
     27: eval(code, test_env)
     28: 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)
     29: doTryCatch(return(expr), name, parentenv, handler)
     30: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     31: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     32: doTryCatch(return(expr), name, parentenv, handler)
     33: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     34: tryCatchList(expr, classes, parentenv, handlers)
     35: 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) { })
     36: test_code(desc, code, env = parent.frame())
     37: test_that("single_sim testing with stansim_data input", { expect_false(dir.exists("testdir")) catch <- capture_output(test_stanfit <- rstan::stan_model(file = "data-raw/simtestreg.stan")) reg_sim <- function(N = 100) { list(N = N, x = rep(0, N), y = rep(0, N)) } reg_data <- reg_sim(100) test_vals <- list(alpha = 100, beta = -5, sigma = 20) catch <- capture_output(ss_data <- simulate_data(file = "data-raw/simtestreg.stan", data_name = "saved stansim_data", input_data = reg_data, nsim = 1, path = "testdir", param_values = test_vals, vars = c("sim_x", "sim_y", "N"), use_cores = 1)) ss_data <- ss_data$dataset expect_true(dir.exists("testdir")) test_stan_args <- list(object = test_stanfit, iter = 500, chains = 4) catch <- capture_output(catch_out <- rstansim:::single_sim(dataset = ss_data, stan_args = test_stan_args, calc_loo = F, parameters = c("alpha", "beta", "sigma"), probs = c(0.025, 0.25, 0.5, 0.75, 0.975), estimates = c("mean", "se_mean", "sd", "n_eff", "Rhat"), stan_warnings = "suppress", cache = F)) expect_type(catch_out, "list") expect_s3_class(catch_out, "stansim_uni") expect_equal(length(catch_out), 10) expect_equal(names(catch_out), c("data_name", "ran_at", "elapsed_time", "stan_inits", "stan_args", "seed", "out_data", "model_name", "model_code", "warnings")) expect_type(catch_out$data_name, "character") is_date <- function(mydate, date.format = "%d/%m/%y") { tryCatch(!is.na(as.Date(mydate, date.format, tz = "UTC")), error = function(err) FALSE) } expect_true(is_date(catch_out$ran_at)) expect_equal(dim(catch_out$elapsed_time), c(test_stan_args$chains, 2)) expect_equal(colnames(catch_out$elapsed_time), c("warmup", "sample")) expect_type(catch_out$stan_inits, "list") expect_equal(length(catch_out$stan_inits), 4) ident <- function(...) { args <- c(...) if (length(args) > 2L) { out <- c(identical(args[1], args[2]), ident(args[-1])) } else { out <- identical(args[1], args[2]) } return(all(out)) } expect_true(ident(catch_out$stan_args[[1]]$iter, catch_out$stan_args[[2]]$iter, catch_out$stan_args[[3]]$iter, catch_out$stan_args[[4]]$iter)) expect_true(ident(catch_out$stan_args[[1]]$thin, catch_out$stan_args[[2]]$thin, catch_out$stan_args[[3]]$thin, catch_out$stan_args[[4]]$thin)) expect_true(ident(catch_out$stan_args[[1]]$warmup, catch_out$stan_args[[2]]$warmup, catch_out$stan_args[[3]]$warmup, catch_out$stan_args[[4]]$warmup)) expect_true(ident(catch_out$stan_args[[1]]$init, catch_out$stan_args[[2]]$init, catch_out$stan_args[[3]]$init, catch_out$stan_args[[4]]$init)) expect_true(ident(catch_out$stan_args[[1]]$algorithm, catch_out$stan_args[[2]]$algorithm, catch_out$stan_args[[3]]$algorithm, catch_out$stan_args[[4]]$algorithm)) expect_true(ident(catch_out$stan_args[[1]]$check_unknown_args, catch_out$stan_args[[2]]$check_unknown_args, catch_out$stan_args[[3]]$check_unknown_args, catch_out$stan_args[[4]]$check_unknown_args)) expect_true(ident(catch_out$stan_args[[1]]$sampling, catch_out$stan_args[[2]]$sampling, catch_out$stan_args[[3]]$sampling, catch_out$stan_args[[4]]$sampling)) expect_type(catch_out$seed, "integer") expect_equal(catch_out$model_name, "simtestreg") expect_type(catch_out$model_code, "character") expect_true(dir.exists("testdir")) unlink("testdir", recursive = T) expect_false(dir.exists("testdir"))})
     38: eval(code, test_env)
     39: eval(code, test_env)
     40: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
     41: doTryCatch(return(expr), name, parentenv, handler)
     42: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     43: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     44: doTryCatch(return(expr), name, parentenv, handler)
     45: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     46: tryCatchList(expr, classes, parentenv, handlers)
     47: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
     48: test_code(NULL, exprs, env)
     49: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
     50: force(code)
     51: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter, { lister$start_file(basename(path)) source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap) end_context() })
     52: FUN(X[[i]], ...)
     53: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
     54: force(code)
     55: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap))
     56: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
     57: 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)
     58: 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)
     59: test_check("rstansim")
     An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 0.1.1
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Loading required package: Rcpp
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    
     *** caught segfault ***
    address 10, cause 'memory not mapped'
    
    Traceback:
     1: FUN(X[[i]], ...)
     2: lapply(name, function(id) { v <- .Internal(getSymbolInfo(as.character(id), PACKAGE, as.logical(withRegistrationInfo))) if (is.null(v)) { msg <- paste("no such symbol", id) if (length(pkgName) && nzchar(pkgName)) msg <- paste(msg, "in package", pkgName) stop(msg, domain = NA) } names(v) <- c("name", "address", "package", "numParameters")[seq_along(v)] v})
     3: getNativeSymbolInfo(name, PACKAGE)
     4: doTryCatch(return(expr), name, parentenv, handler)
     5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     6: tryCatchList(expr, classes, parentenv, handlers)
     7: tryCatch(getNativeSymbolInfo(name, PACKAGE), error = function(e) e)
     8: Module(module, mustStart = TRUE)
     9: .getModulePointer(x)
    10: new("Module", .xData = <environment>)$stan_fit4model7134167217ed_sim_data_model
    11: eval(call("$", mod, paste("stan_fit4", model_cppname, sep = "")))
    12: eval(call("$", mod, paste("stan_fit4", model_cppname, sep = "")))
    13: object@mk_cppmodule(object)
    14: .local(object, ...)
    15: rstan::sampling(object = cmodel, data = input_data, init = list(param_values), iter = nsim, chains = 1, cores = use_cores, warmup = 0, algorithm = "Fixed_param", seed = seed)
    16: rstan::sampling(object = cmodel, data = input_data, init = list(param_values), iter = nsim, chains = 1, cores = use_cores, warmup = 0, algorithm = "Fixed_param", seed = seed)
    17: simulate_internal(cmodel = compiled_model, input_data = input_data, vars = vars, param_values = param_values, nsim = nsim, use_cores = use_cores, sim_drop = sim_drop, seed = seed)
    18: simulate_data(file = "sim_data_model.stan", data_name = "correlated multi-regression", input_data = regression_input_data, param_values = regression_corr_params, vars = c("N", "K", "sim_x", "sim_y"), nsim = 50, path = "reg_data/correlated", seed = 1234)
    19: eval(expr, envir, enclos)
    20: eval(expr, envir, enclos)
    21: withVisible(eval(expr, envir, enclos))
    22: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
    23: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
    24: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    25: evaluate_call(expr, parsed$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)
    26: evaluate::evaluate(...)
    27: 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$render, options))
    28: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)))
    29: block_exec(params)
    30: call_block(x)
    31: process_group.block(group)
    32: process_group(group)
    33: 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$get("infile"), ") ") })
    34: process_file(text, output)
    35: knit(input, text = text, envir = envir, encoding = encoding, quiet = quiet)
    36: knit2html(..., force_v1 = TRUE)
    37: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
    38: vweave(...)
    39: engine$weave(file, quiet = quiet, encoding = enc)
    40: doTryCatch(return(expr), name, parentenv, handler)
    41: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    42: tryCatchList(expr, classes, parentenv, handlers)
    43: 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)})
    44: buildVignettes(dir = "/home/ripley/R/packages/tests32/rstansim.Rcheck/vign_test/rstansim")
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 0.1.1
Check: tests
Result: ERROR
     Running ‘testthat.R’ [252s/415s]
    Running the tests in ‘tests/testthat.R’ failed.
    Last 13 lines of output:
     > Sys.setenv("R_TESTS" = "")
     > library(testthat)
     > library(rstansim)
     Loading required package: Rcpp
     >
     > test_check("rstansim")
    
     *** caught segfault ***
     address 0x107f89aa0, cause 'memory not mapped'
    
     Traceback:
     1: .Call(list(name = "CppObject__finalize", address = <pointer: 0x7fcf56212660>, dll = list(name = "Rcpp", path = "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/Rcpp/libs/Rcpp.so", dynamicLookup = TRUE, handle = <pointer: 0x7fcf5620b0f0>, info = <pointer: 0x7fcf5385df00>), numParameters = 2L), <pointer: 0x7fcf53470440>, .pointer)
     2: x$.self$finalize()
     3: (function (x) x$.self$finalize())(<environment>)
     An irrecoverable exception occurred. R is aborting now ...
Flavor: r-release-osx-x86_64