* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/lavDiag.Rcheck’ * using R Under development (unstable) (2026-01-16 r89305) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) * running under: Fedora Linux 40 (Workstation Edition) * using session charset: UTF-8 * checking for file ‘lavDiag/DESCRIPTION’ ... OK * this is package ‘lavDiag’ version ‘0.1.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘lavDiag’ can be installed ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [15s/16s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... OK * checking examples with --run-donttest ... ERROR Running examples in ‘lavDiag-Ex.R’ failed The error most likely occurred in: > ### Name: augment > ### Title: Augment SEM data with predictions, residuals, SEs/CIs, and > ### ordinal extras > ### Aliases: augment > > ### ** Examples > > # Continuous example > HS.model <- 'visual =~ x1 + x2 + x3 + textual =~ x4 + x5 + x6 + speed =~ x7 + x8 + x9' > fit <- lavaan::cfa(HS.model, + data = lavaan::HolzingerSwineford1939, + meanstructure = TRUE) > augment(fit) # A tibble: 301 × 63 .rid .gid .group visual textual speed .se_visual .se_textual .se_speed 1 1 1 -1.37 -0.0995 0.232 0.475 0.332 0.328 2 2 1 0.0759 -1.20 0.989 0.475 0.332 0.328 3 3 1 -0.561 -2.10 -1.12 0.475 0.332 0.328 4 4 1 0.802 -0.00414 -0.488 0.475 0.332 0.328 5 5 1 -0.745 -0.115 0.372 0.475 0.332 0.328 6 6 1 0.0708 -1.57 1.13 0.475 0.332 0.328 7 7 1 -1.82 0.840 0.208 0.475 0.332 0.328 8 8 1 0.399 -0.118 -0.837 0.475 0.332 0.328 9 9 1 -0.590 0.486 0.339 0.475 0.332 0.328 10 10 1 -1.59 0.201 -0.708 0.475 0.332 0.328 # ℹ 291 more rows # ℹ 54 more variables: x1 , x2 , x3 , x4 , x5 , # x6 , x7 , x8 , x9 , .yhat_x1 , .yhat_x2 , # .yhat_x3 , .yhat_x4 , .yhat_x5 , .yhat_x6 , # .yhat_x7 , .yhat_x8 , .yhat_x9 , .yhat_lwr_x1 , # .yhat_lwr_x2 , .yhat_lwr_x3 , .yhat_lwr_x4 , # .yhat_lwr_x5 , .yhat_lwr_x6 , .yhat_lwr_x7 , … > > ## No test: > # --- Ordinal example (discretize by quantiles; 5 ordered categories) ------- > ord_items <- paste0("x", 1:9) > HS_ord <- lavaan::HolzingerSwineford1939 > for (v in ord_items) { + q <- stats::quantile(HS_ord[[v]], probs = seq(0, 1, length.out = 6), na.rm = TRUE) + q <- unique(q) # guard against duplicate cut points + HS_ord[[v]] <- as.ordered(cut(HS_ord[[v]], breaks = q, include.lowest = TRUE)) + } > > fit_ord <- lavaan::cfa( + HS.model, + data = HS_ord, + ordered = ord_items, + estimator = "WLSMV", + parameterization = "delta", + meanstructure = TRUE + ) > augment(fit_ord) Error in checkNumberOfLocalWorkers(workers) : Attempting to set up 31 localhost parallel workers with only 2 CPU cores available for this R process (per ‘mc.cores’), which could result in a 1550% load. The hard limit is set to 300%. Overusing the CPUs has negative impact on the current R process, but also on all other processes of yours and others running on the same machine. See help("parallelly.maxWorkers.localhost", package = "parallelly") for further explanations and how to override the hard limit that triggered this error. By the way, was parallel::detectCores() used, because the number of workers (31) equals detectCores() - 1? If so, please use parallelly::availableCores() instead Calls: augment ... do.call -> -> checkNumberOfLocalWorkers Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ Running ‘testthat.R’ ERROR 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(lavDiag) > > test_check("lavDiag") Saving _problems/test-augment-13.R Saving _problems/test-lavPredict_parallel-11.R Saving _problems/test-prepare-12.R [ FAIL 3 | WARN 25 | SKIP 1 | PASS 28 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-item_data.R:2:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-augment.R:13:3'): augment works on mixed model (yhat present at least) ── Error in `checkNumberOfLocalWorkers(workers)`: Attempting to set up 31 localhost parallel workers with only 2 CPU cores available for this R process (per 'mc.cores'), which could result in a 1550% load. The hard limit is set to 300%. Overusing the CPUs has negative impact on the current R process, but also on all other processes of yours and others running on the same machine. See help("parallelly.maxWorkers.localhost", package = "parallelly") for further explanations and how to override the hard limit that triggered this error. By the way, was parallel::detectCores() used, because the number of workers (31) equals detectCores() - 1? If so, please use parallelly::availableCores() instead Backtrace: ▆ 1. ├─lavDiag::augment(fit) at test-augment.R:13:3 2. │ └─lavDiag::lavPredict_parallel(...) 3. │ └─lavDiag:::.set_future_plan(plan = plan, workers = workers) 4. │ └─future::plan(future::multisession, workers = pick_workers(workers)) 5. │ └─future (local) plan_set(...) 6. │ └─future:::plan_init(stack[[1]], debug = debug) 7. │ └─future:::makeFutureBackend(evaluator, debug = debug) 8. │ └─base::do.call(factory, args = args, envir = envir) 9. └─future (local) ``(workers = 31L) 10. └─future::ClusterFutureBackend(...) 11. └─clusterRegistry$startCluster(...) 12. └─future (local) makeCluster(workers, ...) 13. ├─base::do.call(makeClusterPSOCK, args = args, quote = TRUE) 14. └─parallelly (local) ``(base::quote(31L), rscript_libs = base::quote(``)) 15. └─parallelly:::checkNumberOfLocalWorkers(workers) ── Error ('test-lavPredict_parallel.R:11:3'): lavPredict_parallel runs on ordinal and mixed (SEs optional) ── Error in `checkNumberOfLocalWorkers(workers)`: Attempting to set up 31 localhost parallel workers with only 2 CPU cores available for this R process (per 'mc.cores'), which could result in a 1550% load. The hard limit is set to 300%. Overusing the CPUs has negative impact on the current R process, but also on all other processes of yours and others running on the same machine. See help("parallelly.maxWorkers.localhost", package = "parallelly") for further explanations and how to override the hard limit that triggered this error. By the way, was parallel::detectCores() used, because the number of workers (31) equals detectCores() - 1? If so, please use parallelly::availableCores() instead Backtrace: ▆ 1. ├─lavDiag::lavPredict_parallel(fit_o, return_type = "data", se = FALSE) at test-lavPredict_parallel.R:11:3 2. │ ├─base::suppressWarnings(...) 3. │ │ └─base::withCallingHandlers(...) 4. │ └─furrr::future_map(...) 5. │ └─furrr:::furrr_map_template(...) 6. │ └─furrr:::furrr_template(...) 7. │ ├─future::nbrOfWorkers() 8. │ └─future:::nbrOfWorkers.NULL() 9. │ └─future::plan("backend") 10. │ └─future:::plan_init(strategy, debug = debug) 11. │ └─future:::makeFutureBackend(evaluator, debug = debug) 12. │ └─base::do.call(factory, args = args, envir = envir) 13. └─future (local) ``(workers = 31L) 14. └─future::ClusterFutureBackend(...) 15. └─clusterRegistry$startCluster(...) 16. └─future (local) makeCluster(workers, ...) 17. ├─base::do.call(makeClusterPSOCK, args = args, quote = TRUE) 18. └─parallelly (local) ``(base::quote(31L), rscript_libs = base::quote(``)) 19. └─parallelly:::checkNumberOfLocalWorkers(workers) ── Error ('test-prepare.R:12:3'): prepare merges branches for mixed model ────── Error in `prepare(fit, length.out = 15)`: Neither continuous nor ordinal branch succeeded - check model/functions. Backtrace: ▆ 1. └─lavDiag::prepare(fit, length.out = 15) at test-prepare.R:12:3 2. └─rlang::abort("Neither continuous nor ordinal branch succeeded - check model/functions.") [ FAIL 3 | WARN 25 | SKIP 1 | PASS 28 ] Error: ! Test failures. Execution halted * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 2 ERRORs See ‘/data/blackswan/ripley/R/packages/tests-devel/lavDiag.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 1:27.12, 63.41 + 23.21