• using R Under development (unstable) (2025-12-24 r89227)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.8 (1)     Debian flang version 21.1.8 (1)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘EFAtools/DESCRIPTION’ ... OK
• this is package ‘EFAtools’ version ‘0.6.1’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/4s] OK
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• checking package dependencies ... OK
• checking if this is a source package ... OK
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• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘EFAtools’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘Debian clang version 21.1.8 (1)’
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
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• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
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• checking R code for possible problems ... [23s/26s] OK
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• checking for unstated dependencies in examples ... OK
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• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [7s/10s] ERROR Running examples in ‘EFAtools-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: OMEGA > ### Title: McDonald's omega > ### Aliases: OMEGA > > ### ** Examples > > > ## Use with an output from the SL function, with type EFAtools > efa_mod <- EFA(test_models$baseline$cormat, N = 500, n_factors = 3, + type = "EFAtools", method = "PAF", rotation = "promax") > sl_mod <- SL(efa_mod, type = "EFAtools", method = "PAF") > > # Two examples how to specify the indicator-to-factor correspondences: > > # Based on a specific salience threshold for the loadings (here: .20): > factor_corres_1 <- sl_mod$sl[, c("F1", "F2", "F3")] >= .2 > > # Or more flexibly (could also be TRUE and FALSE instead of 0 and 1): > factor_corres_2 <- matrix(c(rep(0, 12), rep(1, 6), rep(0, 6), rep(1, 6), + rep(0, 6), rep(1, 6), rep(0, 12)), ncol = 3, + byrow = FALSE) > > OMEGA(sl_mod, type = "EFAtools", factor_corres = factor_corres_1) Omega total, omega hierarchical, omega subscale, H index, explained common variance (ECV), and percent of uncontaminated correlations (PUC) for the general factor (top row) and omegas and H index for the group factors:      tot hier sub H ECV PUC g 0.883 0.740 0.125 0.842 0.659 0.706 F1 0.769 0.500 0.269 0.463 F2 0.763 0.494 0.270 0.472 F3 0.744 0.519 0.225 0.408 > > ## Use with an output from the psych::schmid function, with type psych for > ## OMEGA > schmid_mod <- psych::schmid(test_models$baseline$cormat, nfactors = 3, + n.obs = 500, fm = "pa", rotate = "Promax") > # Find correlation matrix from phi and pattern matrix from psych::schmid output > OMEGA(schmid_mod, type = "psych") Error in xtfrm.data.frame(list(`1` = 0.0378603062522911, `2` = 0.0133470820794105, :   cannot xtfrm data frames Calls: OMEGA -> .OMEGA_FLEX -> xtfrm -> xtfrm.data.frame Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [149s/193s] ERROR   Running ‘testthat.R’ [149s/192s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(EFAtools)   >   > test_check("EFAtools")                                                                                                                                                                          🏃 Extracting data...                                                                                                                                                                       🚶 Reordering factors...                                                                                                                                                                       🏃 Averaging data...                                                                                                                                                                       Done!                                                                                                                                                                          🏃 Extracting data...                                                                                                                                                                       🚶 Reordering factors...                                                                                                                                                                       🏃 Averaging data...                                                                                                                                                                       Done!                                                                                                                                                                          🏃 Extracting data...                                                                                                                                                                       🚶 Reordering factors...                                                                                                                                                                       🏃 Averaging data...                                                                                                                                                                       Done!                                                                                                                                                                          🏃 Extracting data...                                                                                                                                                                       🚶 Reordering factors...                                                                                                                                                                       🏃 Averaging data...                                                                                                                                                                       Done!                                                                                                                                                                          🏃 Extracting data...                                                                                                                                                                       🚶 Reordering factors...                                                                                                                                                                       🏃 Averaging data...                                                                                                                                                                       Done!                                                                                                                                                                          🏃 Extracting data...                                                                                                                                                                       🚶 Reordering factors...                                                                                                                                                                       🏃 Averaging data...                                                                                                                                                                       Done!                                                                                                                                                                          🏃 Extracting data...                                                                                                                                                                       🚶 Reordering factors...                                                                                                                                                                       🏃 Averaging data...                                                                                                                                                                       Done!                                                                                                                                                                          🏃 Extracting data...                                                                                                                                                                       🚶 Reordering factors...                                                                                                                                                                       🏃 Averaging data...                                                                                                                                                                       Done!                                                                                                                                                                          🏃 Extracting data...                                                                                                                                                                       🚶 Reordering factors...                                                                                                                                                                       🏃 Averaging data...                                                                                                                                                                       Done!                                                                                                                                                                          🏃 Extracting data...                                                                                                                                                                       🏃 Averaging data...                                                                                                                                                                       Done!                                                                                                                                                                          🏃 Extracting data...                                                                                                                                                                       🚶 Reordering factors...                                                                                                                                                                       🏃 Averaging data...                                                                                                                                                                       Done!                                                                                                                                                                          🏃 Extracting data...                                                                                                                                                                       🚶 Reordering factors...                                                                                                                                                                       🏃 Averaging data...                                                                                                                                                                       Done!                                                                                                                                                                          🏃 Extracting data...                                                                                                                                                                       🚶 Reordering factors...                                                                                                                                                                       🏃 Averaging data...                                                                                                                                                                       Done!                                                                                                                                                                          🏃 Extracting data...                                                                                                                                                                       🏃 Averaging data...                                                                                                                                                                       Done!                                                                                                                                                                          🏃 Extracting data...                                                                                                                                                                       🏃 Averaging data...                                                                                                                                                                       Done!                                                                                                                                                                          🏃 Extracting data...                                                                                                                                                                       🏃 Averaging data...                                                                                                                                                                       Done!   Saving _problems/test-OMEGA-22.R   Saving _problems/test-OMEGA_helper-173.R   [ FAIL 2 | WARN 0 | SKIP 0 | PASS 2215 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-OMEGA.R:22:1'): (code run outside of `test_that()`) ────────────   Error in `xtfrm.data.frame(structure(list(`1` = 0.0378603062522911, `2` = 0.0133470820794105, `3` = 0.338365397997874), row.names = "V1", class = "data.frame"))`: cannot xtfrm data frames   Backtrace:       ▆    1. └─EFAtools::OMEGA(schmid_mod, type = "psych") at test-OMEGA.R:22:1    2. └─EFAtools:::.OMEGA_FLEX(...)    3. ├─base::xtfrm(`<df[,3]>`)    4. └─base::xtfrm.data.frame(`<df[,3]>`)   ── Error ('test-OMEGA_helper.R:173:1'): (code run outside of `test_that()`) ────   Error in `xtfrm.data.frame(structure(list(`1` = 0.0378603062522911, `2` = 0.0133470820794105, `3` = 0.338365397997874), row.names = "V1", class = "data.frame"))`: cannot xtfrm data frames   Backtrace:       ▆    1. └─EFAtools:::.OMEGA_FLEX(schmid_mod, type = "psych", variance = "correlation") at test-OMEGA_helper.R:173:1    2. ├─base::xtfrm(`<df[,3]>`)    3. └─base::xtfrm.data.frame(`<df[,3]>`)      [ FAIL 2 | WARN 0 | SKIP 0 | PASS 2215 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [140s/159s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘EFAtools.Rmd’ using rmarkdown Quitting from EFAtools.Rmd:254-256 [unnamed-chunk-24] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `xtfrm.data.frame()`: ! cannot xtfrm data frames --- Backtrace:     ▆  1. └─EFAtools::OMEGA(sl_dospert, type = "psych")  2. └─EFAtools:::.OMEGA_FLEX(...)  3. ├─base::xtfrm(`<df[,6]>`)  4. └─base::xtfrm.data.frame(`<df[,6]>`) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'EFAtools.Rmd' failed with diagnostics: cannot xtfrm data frames --- failed re-building ‘EFAtools.Rmd’ --- re-building ‘Replicate_SPSS_psych.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Replicate_SPSS_psych.Rmd’ SUMMARY: processing the following file failed:   ‘EFAtools.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [8s/12s] OK
• checking HTML version of manual ... [8s/13s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 3 ERRORs