• using R Under development (unstable) (2025-01-20 r87609)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 19.1.7     flang-new version 19.1.7
• running under: Fedora Linux 36 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘Surrogate/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘Surrogate’ version ‘3.3.0’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Imports includes 22 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally.
• 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 ‘Surrogate’ can be installed ... [99s/383s] OK See the install log for details.
• checking installed package size ... 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 ... [6s/25s] OK
• checking whether the package can be loaded with stated dependencies ... [5s/21s] OK
• checking whether the package can be unloaded cleanly ... [5s/21s] OK
• checking whether the namespace can be loaded with stated dependencies ... [5s/23s] OK
• checking whether the namespace can be unloaded cleanly ... [6s/26s] OK
• checking loading without being on the library search path ... [6s/27s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘optimx’   All declared Imports should be used.
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [3m/12m] OK
• checking Rd files ... [4s/10s] 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 contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking examples ... [129s/428s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [7m/17m] ERROR   Running ‘testthat.R’ [7m/17m] 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(Surrogate)   >   > test_check("Surrogate")   Loading required namespace: cubature   Loading required namespace: FNN   Loading required namespace: parallel   [1] "Starting parallel simulations"   [1] "Finishing parallel simulations"   Loading required namespace: copula   Loading required namespace: fitdistrplus   Loading required namespace: stringr   [ FAIL 19 | WARN 0 | SKIP 9 | PASS 28 ]      ══ Skipped tests (9) ═══════════════════════════════════════════════════════════   • On CRAN (9): 'test-MetaAnalyticSurvBin.R:3:13',     'test-MetaAnalyticSurvCat.R:3:13', 'test-MetaAnalyticSurvCont.R:3:13',     'test-MetaAnalyticSurvSurv.R:3:13', 'test-fit_model_SurvSurv.R:37:13',     'test-fit_model_SurvSurv.R:58:13', 'test-goodness_of_fit_SurvSurv.R:19:13',     'test-sensitivity_analysis_SurvSurv.R:44:3',     'test-sensitivity_intervals.R:94:3'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Failure ('test-ICA_BinCont_copula.R:9:3'): sample_dvine() works with clayton copula ──   `output_values` (`actual`) not equal to `expected_values` (`expected`).        `actual`: 0.99131 0.47209 0.65521 0.98636   `expected`: 0.99153 0.02533 0.52019 0.06634   ── Failure ('test-ICA_BinCont_copula.R:35:3'): sample_deltas_BinCont() works with clayton copula ──   `output_values` (`actual`) not equal to `expected_values` (`expected`).        `actual`: 1.76 0.35 1.00 0.00   `expected`: 1.20 1.00 0.00 0.00   ── Failure ('test-ICA_BinCont_copula.R:63:3'): estimate_ICA_BinCont() works in a sample example ──   `output_values` (`actual`) not equal to `expected_values` (`expected`).        `actual`: 1.76 0.35 1.00 0.00   `expected`: 1.20 1.00 0.00 0.00   ── Failure ('test-ICA_BinCont_copula.R:91:3'): compute_ICA_BinCont() works in a sample example ──   `output_values` (`actual`) not equal to `expected_values` (`expected`).        `actual`: 0.2638 -0.5661 0.3336 0.7359   `expected`: 0.2505 -0.5384 0.3952 0.7446   ── Failure ('test-ICA_SurvSurv_copula.R:29:3'): compute_ICA_SurvSurv works ─────   `output_vector` (`actual`) not equal to `check_vector` (`expected`).        `actual`: 0.3354 0.4093 0.8920 0.8380   `expected`: 0.3299 0.3859 0.8902 0.8350   ── Failure ('test-ICA_SurvSurv_copula.R:60:3'): compute_ICA_SurvSurv works for different unidentifiable copulas ──   `output_vector` (`actual`) not equal to `check_vector` (`expected`).        `actual`: 0.4237 0.2766 0.6657 0.5154   `expected`: 0.4410 0.3103 0.6764 0.5115   ── Failure ('test-ITCI-Dvine-inference-utils.R:16:3'): Delta method based on numerical derivatives works ──   `estimated_variance` (`actual`) not equal to matrix(0.309301300833, nrow = 1, ncol = 1) (`expected`).      actual vs expected                        [,1]   - actual[1, ] 0.6785348   + expected[1, ] 0.3093013   ── Failure ('test-ITCI-Dvine-inference-utils.R:49:3'): Resampling method for the ICA based on fitted model summary information works ──   c(mean_ICA, sd_ICA) (`actual`) not equal to c(0.99096747638744, 0.00145160206983) (`expected`).        `actual`: 0.991708 0.001429   `expected`: 0.990967 0.001452   ── Failure ('test-ITCI-Dvine-inference-utils.R:50:3'): Resampling method for the ICA based on fitted model summary information works ──   c(mean_ICA_p, sd_ICA_p) (`actual`) not equal to c(0.99096747638744, 0.00145160206983) (`expected`).        `actual`: 0.991708 0.001429   `expected`: 0.990967 0.001452   ── Failure ('test-sensitivity_analysis_BinCont_copula.R:14:13'): sensitivity_analysis_BinCont_copula() works in a simplified setting ──   sens_results[, 1] (`actual`) not equal to c(0.407801974151, 0.311636096417) (`expected`).        `actual`: 0.3917 0.3080   `expected`: 0.4078 0.3116   ── Failure ('test-sensitivity_analysis_BinCont_copula.R:35:13'): sensitivity_analysis_BinCont_copula() works in a simplified setting with limits in the sensitivity analysis ──   sens_results[, 1] (`actual`) not equal to c(0.381826406323, 0.301121119697) (`expected`).        `actual`: 0.392 0.291   `expected`: 0.382 0.301   ── Failure ('test-sensitivity_analysis_SurvSurv.R:18:3'): sensitivity_analysis_SurvSurv_copula() works on a single core with Clayton copula ──   `output_vector` (`actual`) not equal to `check_vector` (`expected`).        `actual`: 0.991904525 0.995780207 1.374917943   `expected`: 0.988990899 0.993308293 1.374917943   ── Failure ('test-sensitivity_analysis_SurvSurv.R:38:3'): sensitivity_analysis_SurvSurv_copula() works with variable number of knots ──   `output_vector` (`actual`) not equal to `check_vector` (`expected`).        `actual`: 0.975790156 0.970569834 1.374917943   `expected`: 0.979074242 0.971166765 1.374917943   ── Failure ('test-sensitivity_analysis_SurvSurv.R:80:3'): sensitivity_analysis_SurvSurv_copula() works on a single core with variable copula ──   `output_vector` (`actual`) not equal to `check_vector` (`expected`).        `actual`: 0.970608529 0.964266929 1.374917943   `expected`: 0.973975832 0.972747027 1.374917943   ── Failure ('test-sensitivity_analysis_SurvSurv.R:117:3'): sensitivity_analysis_SurvSurv_copula() works on a single core with Clayton copula and four different unidentifiable copulas ──   c(sens_results$ICA[1], sens_results$sp_rho[1], sens_results$c23[1]) (`actual`) not equal to c(0.996814266963, 0.995511262378, 0.436161760666) (`expected`).        `actual`: 0.997023687 0.995343606 0.436161761   `expected`: 0.996814267 0.995511262 0.436161761   ── Failure ('test-sensitivity_analysis_SurvSurv.R:151:3'): sensitivity_analysis_SurvSurv_copula() wth restricted survival times and Spearman's rho as ICA ──   `output_vector` (`actual`) not equal to `check_vector` (`expected`).        `actual`: 0.822232 0.996771 1.682037   `expected`: 0.822136 0.995515 1.682037   ── Failure ('test-sensitivity_intervals.R:45:3'): Intervals of ignorance and uncertainty are correctly computed ──   c(...) (`actual`) not equal to c(...) (`expected`).          actual | expected   [1] 0.835910421 | 0.835910421 [1]   [2] 0.997707840 | 0.997707840 [2]   [3] 0.771344327 - 0.748958557 [3]   [4] 0.996707340 - 0.997291086 [4]   [5] 0.777426823 - 0.754652671 [5]   [6] 0.996552084 - 0.997185131 [6]   ── Failure ('test-sensitivity_intervals.R:60:3'): Intervals of ignorance and uncertainty are correctly computed ──   c(...) (`actual`) not equal to c(...) (`expected`).          actual | expected   [1] 0.642646510 | 0.642646510 [1]   [2] 0.991589288 | 0.991589288 [2]   [3] 0.562796108 - 0.504365537 [3]   [4] 0.989819380 - 0.991103511 [4]   [5] 0.564156839 - 0.521834842 [5]   [6] 0.989592088 - 0.990989206 [6]   ── Failure ('test-sensitivity_intervals.R:75:3'): Intervals of ignorance and uncertainty are correctly computed ──   c(...) (`actual`) not equal to c(...) (`expected`).          actual | expected   [1] 0.751294689 | 0.751294689 [1]   [2] 0.820984966 | 0.820984966 [2]   [3] 0.727620865 - 0.711347431 [3]   [4] 0.820958783 - 0.820793874 [4]   [5] 0.728769400 - 0.712601776 [5]   [6] 0.820940724 - 0.820715995 [6]      [ FAIL 19 | WARN 0 | SKIP 9 | PASS 28 ]   Deleting unused snapshots:   • goodness_of_fit_SurvSurv/marginal-survival-functions-gof.svg   • goodness_of_fit_SurvSurv/prob-of-dying-wo-progression-gof.svg   Error: Test failures   Execution halted
• checking PDF version of manual ... [26s/44s] OK
• checking HTML version of manual ... [26s/35s] OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR, 1 NOTE