betaselectr

*

*

*

*

tests

  Running ‘testthat.R’ [4s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(betaselectr)
  > 
  > test_check("betaselectr")
  Starting 2 test processes.
  > test-lav_betaselect.R: This is lavaan 0.6-21
  > test-lav_betaselect.R: lavaan is FREE software! Please report any bugs.
  > test-lav_betaselect_check.R: This is lavaan 0.6-21
  > test-lav_betaselect_check.R: lavaan is FREE software! Please report any bugs.
  > test-lav_betaselect_user_2.R: 
  > test-lav_betaselect_user_2.R:  *** caught segfault ***
  > test-lav_betaselect_user_2.R: address 0x1, cause 'invalid permissions'
  > test-lav_betaselect_user_2.R: 
  > test-lav_betaselect_user_2.R: Traceback:
  > test-lav_betaselect_user_2.R:  1: eigen(S, symmetric = TRUE)
  > test-lav_betaselect_user_2.R:  2: lav_matrix_symmetric_inverse(S = Sigma, logdet = TRUE, Sinv.method = Sinv.method)
  > test-lav_betaselect_user_2.R:  3: lav_mvnorm_loglik_samplestats(sample.mean = lavsamplestats@mean[[g]],     sample.cov = lavsamplestats@cov[[g]], sample.nobs = lavsamplestats@nobs[[g]],     Mu = Mu, Sigma = lavimplied$cov[[g]], x.idx = lavsamplestats@x.idx[[g]],     x.mean = lavsamplestats@mean.x[[g]], x.cov = lavsamplestats@cov.x[[g]],     Sinv.method = "eigen", Sigma.inv = NULL)
  > test-lav_betaselect_user_2.R:  4: lav_model_loglik(lavdata = lavdata, lavsamplestats = lavsamplestats,     lavh1 = lavh1, lavimplied = lavimplied, lavmodel = lavmodel,     lavoptions = lavoptions)
  > test-lav_betaselect_user_2.R:  5: lav_lavaan_step12_loglik(lavoptions = lavoptions, lavdata = lavdata,     lavsamplestats = lavsamplestats, lavh1 = lavh1, lavimplied = lavimplied,     lavmodel = lavmodel)
  > test-lav_betaselect_user_2.R:  6: lavaan::lavaan(slotOptions = slot_opt1, slotParTable = slot_pat1,     slotModel = slot_mod1, slotSampleStats = slot_smp, slotData = slot_dat)
  > test-lav_betaselect_user_2.R:  7: func(x * (0 + (0+1i)), ...)
  > test-lav_betaselect_user_2.R:  8: doTryCatch(return(expr), name, parentenv, handler)
  > test-lav_betaselect_user_2.R:  9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  > test-lav_betaselect_user_2.R: 10: tryCatchList(expr, classes, parentenv, handlers)
  > test-lav_betaselect_user_2.R: 11: 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, nlines = 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))})
  > test-lav_betaselect_user_2.R: 12: try(func(x * (0 + (0+1i)), ...), silent = TRUE)
  > test-lav_betaselect_user_2.R: 13: lavaan::lav_func_jacobian_complex(func = std_fct_v, x = fit_est)
  > test-lav_betaselect_user_2.R: 14: std_se_delta_all(std_fct = std_fct, std_fct_v = std_fct_v, fit_est = fit_est,     fit_vcov = fit_vcov, method = delta_method, progress = progress)
  > test-lav_betaselect_user_2.R: 15: lav_betaselect(fit, standardized = TRUE, not_to_standardize = "x3",     std_se = "delta", ci = TRUE, progress = FALSE)
  > test-lav_betaselect_user_2.R: 16: system.time(out_noy <- lav_betaselect(fit, standardized = TRUE,     not_to_standardize = "x3", std_se = "delta", ci = TRUE, progress = FALSE))
  > test-lav_betaselect_user_2.R: 17: eval(code, test_env)
  > test-lav_betaselect_user_2.R: 18: eval(code, test_env)
  > test-lav_betaselect_user_2.R: 19: withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt)
  > test-lav_betaselect_user_2.R: 20: doTryCatch(return(expr), name, parentenv, handler)
  > test-lav_betaselect_user_2.R: 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  > test-lav_betaselect_user_2.R: 22: tryCatchList(expr, classes, parentenv, handlers)
  > test-lav_betaselect_user_2.R: 23: tryCatch(withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {
  > test-lav_betaselect_user_2.R:     snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
  > test-lav_betaselect_user_2.R: 24: doWithOneRestart(return(expr), restart)
  > test-lav_betaselect_user_2.R: 25: withOneRestart(expr, restarts[[1L]])
  > test-lav_betaselect_user_2.R: 26: withRestarts(tryCatch(withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt), error = handle_fatal),     end_test = function() {    })
  > test-lav_betaselect_user_2.R: 27: test_code(code, parent.frame())
  > test-lav_betaselect_user_2.R: 28: test_that("User parameters", {    system.time(out_noy <- lav_betaselect(fit, standardized = TRUE,         not_to_standardize = "x3", std_se = "delta", ci = TRUE,         progress = FALSE))    ind <- indirect_effect(x = "x1", y = "x3", m = "x2", fit = fit,         standardized_x = TRUE)    expect_equal(out_noy$std.p[6], coef(ind), ignore_attr = TRUE)})
  > test-lav_betaselect_user_2.R: 29: eval(code, test_env)
  > test-lav_betaselect_user_2.R: 30: eval(code, test_env)
  > test-lav_betaselect_user_2.R: 31: withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt)
  > test-lav_betaselect_user_2.R: 32: doTryCatch(return(expr), name, parentenv, handler)
  > test-lav_betaselect_user_2.R: 33: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  > test-lav_betaselect_user_2.R: 34: tryCatchList(expr, classes, parentenv, handlers)
  > test-lav_betaselect_user_2.R: 35: tryCatch(withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
  > test-lav_betaselect_user_2.R: 36: doWithOneRestart(return(expr), restart)
  > test-lav_betaselect_user_2.R: 37: withOneRestart(expr, restarts[[1L]])
  > test-lav_betaselect_user_2.R: 38: withRestarts(tryCatch(withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt), error = handle_fatal),     end_test = function() {    })
  > test-lav_betaselect_user_2.R: 39: test_code(code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
  > test-lav_betaselect_user_2.R: 40: source_file(path, env = env(env), desc = desc, shuffle = shuffle,     error_call = error_call)
  > test-lav_betaselect_user_2.R: 41: test_one_file(path, env = the$testing_env, shuffle = shuffle)
  > test-lav_betaselect_user_2.R: 42: doTryCatch(return(expr), name, parentenv, handler)
  > test-lav_betaselect_user_2.R: 43: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  > test-lav_betaselect_user_2.R: 44: tryCatchList(expr, classes, parentenv, handlers)
  > test-lav_betaselect_user_2.R: 45: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  > test-lav_betaselect_user_2.R: 46: with_reporter(multi, test_one_file(path, env = the$testing_env,     shuffle = shuffle))
  > test-lav_betaselect_user_2.R: 47: asNamespace("testthat")$queue_task(path, shuffle)
  > test-lav_betaselect_user_2.R: 48: (function (path, shuffle) {    asNamespace("testthat")$queue_task(path, shuffle)})(base::quote("test-lav_betaselect_user_2.R"), base::quote(FALSE))
  > test-lav_betaselect_user_2.R: 49: (function (what, args, quote = FALSE, envir = parent.frame()) {    if (!is.list(args))         stop("second argument must be a list")    if (quote)         args <- lapply(args, enquote)    .Internal(do.call(what, args, envir))})(base::quote(function (path, shuffle) {    asNamespace("testthat")$queue_task(path, shuffle)}), base::quote(list("test-lav_betaselect_user_2.R", FALSE)),     envir = base::quote(<environment>), quote = base::quote(TRUE))
  > test-lav_betaselect_user_2.R: 50: base::do.call(base::do.call, base::c(base::readRDS("/Volumes/Temp/tmp/RtmpLQIavd/callr-fun-46465ebdad0d"),     base::list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv,     quote = TRUE)
  > test-lav_betaselect_user_2.R: 51: base::saveRDS(base::do.call(base::do.call, base::c(base::readRDS("/Volumes/Temp/tmp/RtmpLQIavd/callr-fun-46465ebdad0d"),     base::list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv,     quote = TRUE), file = "/Volumes/Temp/tmp/RtmpLQIavd/callr-rs-result-464676ac6112",     compress = FALSE)
  > test-lav_betaselect_user_2.R: 52: base::withCallingHandlers({    {        NULL        NULL    }    base::saveRDS(base::do.call(base::do.call, base::c(base::readRDS("/Volumes/Temp/tmp/RtmpLQIavd/callr-fun-46465ebdad0d"),         base::list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv,         quote = TRUE), file = "/Volumes/Temp/tmp/RtmpLQIavd/callr-rs-result-464676ac6112",         compress = FALSE)    base::flush(base::stdout())    base::flush(base::stderr())    {        NULL        NULL    }    base::invisible()}, error = function(e) {    {        callr_data <- base::as.environment("tools:callr")$`__callr_data__`        err <- callr_data$err        if (FALSE) {            base::assign(".Traceback", base::.traceback(4), envir = callr_data)            utils::dump.frames("__callr_dump__")            base::assign(".Last.dump", .GlobalEnv$`__callr_dump__`,                 envir = callr_data)            base::rm("__callr_dump__", envir = .GlobalEnv)        }        e <- err$process_call(e)        e2 <- err$new_error("error in callr subprocess")        class <- base::class        class(e2) <- base::c("callr_remote_error", class(e2))        e2 <- err$add_trace_back(e2)        cut <- base::which(e2$trace$scope == "global")[1]        if (!base::is.na(cut)) {            e2$trace <- e2$trace[-(1:cut), ]        }        base::saveRDS(base::list("error", e2, e), file = base::paste0("/Volumes/Temp/tmp/RtmpLQIavd/callr-rs-result-464676ac6112",             ".error"))    }}, interrupt = function(e) {    {        callr_data <- base::as.environment("tools:callr")$`__callr_data__`        err <- callr_data$err        if (FALSE) {            base::assign(".Traceback", base::.traceback(4), envir = callr_data)            utils::dump.frames("__callr_dump__")            base::assign(".Last.dump", .GlobalEnv$`__callr_dump__`,                 envir = callr_data)            base::rm("__callr_dump__", envir = .GlobalEnv)        }        e <- err$process_call(e)        e2 <- err$new_error("error in callr subprocess")        class <- base::class        class(e2) <- base::c("callr_remote_error", class(e2))        e2 <- err$add_trace_back(e2)        cut <- base::which(e2$trace$scope == "global")[1]        if (!base::is.na(cut)) {            e2$trace <- e2$trace[-(1:cut), ]        }        base::saveRDS(base::list("error", e2, e), file = base::paste0("/Volumes/Temp/tmp/RtmpLQIavd/callr-rs-result-464676ac6112",             ".error"))    }}, callr_message = function(e) {    base::try({        pxlib <- base::as.environment("tools:callr")$`__callr_data__`$pxlib        if (base::is.null(e$code))             e$code <- "301"
  > test-lav_betaselect_user_2.R:         msg <- base::paste0("base64::", pxlib$base64_encode(base::serialize(e,             NULL)))        data <- base::paste0(e$code, " ", base::nchar(msg), "\n",             msg)        pxlib$write_fd(3L, data)        if (base::inherits(e, "cli_message") && !base::is.null(base::findRestart("cli_message_handled"))) {            base::invokeRestart("cli_message_handled")        }        else if (base::inherits(e, "message") && !base::is.null(base::findRestart("muffleMessage"))) {            base::invokeRestart("muffleMessage")        }    })})
  > test-lav_betaselect_user_2.R: 53: doTryCatch(return(expr), name, parentenv, handler)
  > test-lav_betaselect_user_2.R: 54: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  > test-lav_betaselect_user_2.R: 55: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  > test-lav_betaselect_user_2.R: 56: doTryCatch(return(expr), name, parentenv, handler)
  > test-lav_betaselect_user_2.R: 57: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  > test-lav_betaselect_user_2.R: 58: tryCatchList(expr, classes, parentenv, handlers)
  > test-lav_betaselect_user_2.R: 59: base::tryCatch(base::withCallingHandlers({    {        NULL        NULL    }    base::saveRDS(base::do.call(base::do.call, base::c(base::readRDS("/Volumes/Temp/tmp/RtmpLQIavd/callr-fun-46465ebdad0d"),         base::list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv,         quote = TRUE), file = "/Volumes/Temp/tmp/RtmpLQIavd/callr-rs-result-464676ac6112",         compress = FALSE)    base::flush(base::stdout())    base::flush(base::stderr())    {        NULL        NULL    }    base::invisible()}, error = function(e) {    {        callr_data <- base::as.environment("tools:callr")$`__callr_data__`        err <- callr_data$err        if (FALSE) {            base::assign(".Traceback", base::.traceback(4), envir = callr_data)            utils::dump.frames("__callr_dump__")            base::assign(".Last.dump", .GlobalEnv$`__callr_dump__`,                 envir = callr_data)            base::rm("__callr_dump__", envir = .GlobalEnv)        }        e <- err$process_call(e)        e2 <- err$new_error("error in callr subprocess")        class <- base::class        class(e2) <- base::c("callr_remote_error", class(e2))        e2 <- err$add_trace_back(e2)        cut <- base::which(e2$trace$scope == "global")[1]        if (!base::is.na(cut)) {            e2$trace <- e2$trace[-(1:cut), ]        }        base::saveRDS(base::list("error", e2, e), file = base::paste0("/Volumes/Temp/tmp/RtmpLQIavd/callr-rs-result-464676ac6112",             ".error"))    }}, interrupt = function(e) {    {        callr_data <- base::as.environment("tools:callr")$`__callr_data__`        err <- callr_data$err        if (FALSE) {            base::assign(".Traceback", base::.traceback(4), envir = callr_data)            utils::dump.frames("__callr_dump__")            base::assign(".Last.dump", .GlobalEnv$`__callr_dump__`,                 envir = callr_data)            base::rm("__callr_dump__", envir = .GlobalEnv)        }        e <- err$process_call(e)        e2 <- err$new_error("error in callr subprocess")        class <- base::class        class(e2) <- base::c("callr_remote_error", class(e2))        e2 <- err$add_trace_back(e2)        cut <- base::which(e2$trace$scope == "global")[1]        if (!base::is.na(cut)) {            e2$trace <- e2$trace[-(1:cut), ]        }        base::saveRDS(base::list("error", e2, e), file = base::paste0("/Volumes/Temp/tmp/RtmpLQIavd/callr-rs-result-464676ac6112",             ".error"))    }}, callr_message = function(e) {    base::try({        pxlib <- base::as.environment("tools:callr")$`__callr_data__`$pxlib        if (base::is.null(e$code))             e$code <- "301"        msg <- base::paste0("base64::", pxlib$base64_encode(base::serialize(e,             NULL)))        data <- base::paste0(e$code, " ", base::nchar(msg), "\n",             msg)        pxlib$write_fd(3L, data)        if (base::inherits(e, "cli_message") && !base::is.null(base::findRestart("cli_message_handled"))) {            base::invokeRestart("cli_message_handled")        }        else if (base::inherits(e, "message") && !base::is.null(base::findRestart("muffleMessage"))) {            base::invokeRestart("muffleMessage")        }    })}), error = function(e) {    {        NULL        NULL    }    if (FALSE) {        base::try(base::stop(e))    }    else {        base::invisible()    }}, interrupt = function(e) {    {        NULL        NULL    }    if (FALSE) {        e    }    else {        base::invisible()    }})
  > test-lav_betaselect_user_2.R: An irrecoverable exception occurred. R is aborting now ...
  
  Error:
  ! testthat subprocess exited in file 'test-lav_betaselect_user_2.R'.
  Caused by error:
  ! R session crashed with exit code -11
  Backtrace:
       ▆
    1. └─testthat::test_check("betaselectr")
    2.   └─testthat::test_dir(...)
    3.     └─testthat:::test_files(...)
    4.       └─testthat:::test_files_parallel(...)
    5.         ├─withr::with_dir(...)
    6.         │ └─base::force(code)
    7.         ├─testthat::with_reporter(...)
    8.         │ └─base::tryCatch(...)
    9.         │   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   10.         │     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   11.         │       └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   12.         └─testthat:::parallel_event_loop_chunky(queue, reporters, ".")
   13.           └─queue$poll(Inf)
   14.             └─base::lapply(...)
   15.               └─testthat (local) FUN(X[[i]], ...)
   16.                 └─private$handle_error(msg, i)
   17.                   └─cli::cli_abort(...)
   18.                     └─rlang::abort(...)
  Execution halted

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