• using R Under development (unstable) (2025-11-13 r89015)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)     GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘hdcuremodels/DESCRIPTION’ ... OK
• this is package ‘hdcuremodels’ version ‘0.0.5’
• 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 ‘hdcuremodels’ can be installed ... [31s/80s] OK See the install log for details.
• checking package directory ... OK
• checking ‘build’ 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/16s] OK
• checking whether the package can be loaded with stated dependencies ... [5s/13s] OK
• checking whether the package can be unloaded cleanly ... [5s/15s] OK
• checking whether the namespace can be loaded with stated dependencies ... [5s/16s] OK
• checking whether the namespace can be unloaded cleanly ... [6s/16s] OK
• checking loading without being on the library search path ... [6s/16s] OK
• checking use of S3 registration ... 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 ... [54s/163s] 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 contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [207s/513s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [10m/27m] ERROR   Running ‘testthat.R’ [10m/27m] 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(hdcuremodels)   >   > test_check("hdcuremodels")   Fold 1 out of 2 training...      Fold 2 out of 2 training...      Selected lambda for incidence: 0.083      Selected lambda for latency: 0.083      Maximum C-statistic: 0.724278947141186      Fitting a final model...      Fold 1 out of 2 training...      Fold 2 out of 2 training...      Selected lambda for incidence: 0.062      Selected lambda for latency: 0.062      Maximum C-statistic: 0.756490658082704      Fitting a final model...      Fold 1 out of 2 training...      Fold 2 out of 2 training...      Selected lambda for incidence: 0.062      Selected lambda for latency: 0.062      Maximum C-statistic: 0.756012758916735      Fitting a final model...      Fold 1 out of 2 training...      Fold 2 out of 2 training...      Selected step: 297      Maximum C-statistic: 0.770985658659945      Fitting a final model...      Fold 1 out of 2 training...      Fold 2 out of 2 training...      Selected step: 434      Maximum C-statistic: 0.734125636924359      Fitting a final model...      Fold 1 out of 2 training...      Fold 2 out of 2 training...      Selected lambda for incidence: 0.09      Selected lambda for latency: 0.09      Maximum C-statistic: 0.691812421420305      Fitting a final model...      Fold 1 out of 2 training...      Fold 2 out of 2 training...      Selected lambda for incidence: 0.105      Selected lambda for latency: 0.105      Maximum C-statistic: 0.715520083276069      Fitting a final model...      Fold 1 out of 2 training...      Fold 2 out of 2 training...      Selected step: 27      Maximum C-statistic: 0.674984053587649      Fitting a final model...      Fold 1 out of 2 training...      Fold 2 out of 2 training...      Selected step: 3      Maximum C-statistic: 0.697702519726813      Fitting a final model...         Family: Cox   Algorithm: EM         Family: Cox   Algorithm: EM      Saving _problems/test-formula-11.R   Saving _problems/test-logLik-11.R   Saving _problems/test-nobs-11.R   Fold 1 out of 2 training...      Fold 2 out of 2 training...      Selected step: 27      Maximum C-statistic: 0.674984053587649      Fitting a final model...      Fold 1 out of 2 training...      Fold 2 out of 2 training...      Selected lambda for incidence: 0.155      Selected lambda for latency: 0.155      Maximum C-statistic: 0.635331032165219      Fitting a final model...      Fold 1 out of 2 training...      Fold 2 out of 2 training...      Selected lambda for incidence: 0.083      Selected lambda for latency: 0.083      Maximum C-statistic: 0.724278947141186      Fitting a final model...      mixturecure object fit using Weibull GMIFS algorithm      $b_path        U1 U2 X1 X2 X3 X4   [1,] 0 0 0.01 0 0 0   [2,] 0 0 0.02 0 0 0   [3,] 0 0 0.03 0 0 0   [4,] 0 0 0.04 0 0 0   [5,] 0 0 0.05 0 0 0   [6,] 0 0 0.06 0 0 0   1274 more rows   6 more columns      $beta_path        U1 U2 X1 X2 X3 X4   [1,] 0 0 0.01 0 0 0.00   [2,] 0 0 0.02 0 0 0.00   [3,] 0 0 0.03 0 0 0.00   [4,] 0 0 0.03 0 0 0.01   [5,] 0 0 0.03 0 0 0.02   [6,] 0 0 0.03 0 0 0.03   1274 more rows   6 more columns      $rate    1.74771 1.747557 1.745463 1.776432 1.806308 1.835547   1274 more elements      $alpha    0.5120896 0.5130922 0.5131297 0.5149383 0.5167088 0.51841   1274 more elements      Fold 1 out of 2 training...      Fold 2 out of 2 training...      Selected lambda for incidence: 0.083      Selected lambda for latency: 0.083      Maximum C-statistic: 0.724278947141186      Fitting a final model...      mixturecure object fit using Cox EM algorithm      $b    0 0 0 0 0 0   6 more elements      $beta    0 0 0.8829866 0 0.3677159 0   6 more elements      Fold 1 out of 2 training...      Fold 2 out of 2 training...      Selected lambda for incidence: 0.062      Selected lambda for latency: 0.062      Maximum C-statistic: 0.756490658082704      Fitting a final model...      mixturecure object fit using Weibull EM algorithm      $b    0 0 0.3534216 -0.1938579 0 -0.4778904   6 more elements      $beta    0 0 0 0 0 0   6 more elements      $rate    5.125488      $alpha    0.897226   Mixture cure model fit using the EM algorithm      Number of non-zero incidence covariates at minimum AIC: 0      Number of non-zero latency covariates at minimum AIC: 17      Optimal step for selected information criterion: EM algorithm        at step = 51 logLik = -118.896956094066        at step = 51 AIC = 273.793912188132        at step = 51 mAIC = 490.199530466681        at step = 51 cAIC = 290.4768390174        at step = 51 BIC = 311.492114308129        at step = 51 mBIC = 453.037837086205        at step = 51 EBIC = 370.050413661889      Mixture cure model fit using the EM algorithm      Number of non-zero incidence covariates at minimum AIC: 0      Number of non-zero latency covariates at minimum AIC: 17      Optimal step for selected information criterion: EM algorithm        at step = 51 logLik = -118.896956094066        at step = 51 AIC = 273.793912188132        at step = 51 mAIC = 490.199530466681        at step = 51 cAIC = 290.4768390174        at step = 51 BIC = 311.492114308129        at step = 51 mBIC = 453.037837086205        at step = 51 EBIC = 370.050413661889      Fold 1 out of 2 training...      Fold 2 out of 2 training...      Selected lambda for incidence: 0.054      Selected lambda for latency: 0.054      Maximum C-statistic: 0.703222725537594      Fitting a final model...      Mixture cure model fit using the EM algorithm      using cross-validation      Number of non-zero incidence covariates: 3      Number of non-zero latency covariates: 26      Mixture cure model fit using the EM algorithm      using cross-validation      Number of non-zero incidence covariates: 3      Number of non-zero latency covariates: 26      [ FAIL 3 | WARN 0 | SKIP 0 | PASS 552 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-formula.R:11:3'): formula function works correctly ─────────────   Error in `expect(is.call(formula(fit)))`: `failure_message` must be a character vector, not absent.   Backtrace:       ▆    1. └─testthat::expect(failure_message = <empty>) at test-formula.R:11:3    2. └─testthat:::check_character(failure_message)    3. └─testthat:::stop_input_type(...)    4. └─rlang::abort(message, ..., call = call, arg = arg)   ── Error ('test-logLik.R:11:3'): logLik function works correctly ───────────────   Error in `expect(round(logLik(fit), 5), -9.22893)`: `ok` must be `TRUE` or `FALSE`, not a <logLik> object.   Backtrace:       ▆    1. └─testthat::expect(ok = round(logLik(fit), 5)) at test-logLik.R:11:3    2. └─testthat:::check_bool(ok)    3. └─testthat:::stop_input_type(...)    4. └─rlang::abort(message, ..., call = call, arg = arg)   ── Error ('test-nobs.R:11:3'): nobs function works correctly ───────────────────   Error in `expect(nobs(fit), 60)`: `ok` must be `TRUE` or `FALSE`, not the number 60.   Backtrace:       ▆    1. └─testthat::expect(ok = nobs(fit)) at test-nobs.R:11:3    2. └─testthat:::check_bool(ok)    3. └─testthat:::stop_input_type(...)    4. └─rlang::abort(message, ..., call = call, arg = arg)      [ FAIL 3 | WARN 0 | SKIP 0 | PASS 552 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [58s/168s] OK
• checking PDF version of manual ... [10s/23s] OK
• checking HTML version of manual ... [9s/24s] OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR