• using R Under development (unstable) (2025-11-19 r89040)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.5 (1)     Debian flang version 21.1.5 (1)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘hdcuremodels/DESCRIPTION’ ... OK
• this is package ‘hdcuremodels’ version ‘0.0.5’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/2s] OK
• 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 ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [4s/6s] OK
• checking whether the package can be loaded with stated dependencies ... [3s/5s] OK
• checking whether the package can be unloaded cleanly ... [4s/6s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/4s] OK
• checking whether the namespace can be unloaded cleanly ... [4s/5s] OK
• checking loading without being on the library search path ... [4s/6s] 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 ... [36s/45s] OK
• checking Rd files ... [1s/1s] 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 ... [0s/1s] 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 ... [121s/152s] OK Examples with CPU (user + system) or elapsed time > 5s                       user system elapsed cv_curegmifs 13.253 0.014 16.755 cv_cureem 12.817 0.063 15.707 auc_mcm 6.668 0.164 8.561 coef.mixturecure 6.659 0.046 8.139 plot.mixturecure 6.705 0.000 8.972 concordance_mcm 6.614 0.047 8.743 formula.mixturecure 6.550 0.020 8.757 family.mixturecure 6.536 0.031 8.011 curegmifs 6.536 0.004 8.573 print.mixturecure 6.517 0.000 8.027 predict.mixturecure 6.502 0.004 7.816 nobs.mixturecure 6.502 0.000 8.310 summary.mixturecure 6.490 0.000 7.292 dim.mixturecure 6.438 0.004 7.858 logLik.mixturecure 6.390 0.004 7.729
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [343s/412s] ERROR   Running ‘testthat.R’ [342s/412s] 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: 0.756490658089751      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: 0.756012758893876      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: 0.734125636924605      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: 0.691812421454834      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: 0.71552008323144      Fitting a final model...      Fold 1 out of 2 training...      Fold 2 out of 2 training...      Selected step: 27      Maximum C-statistic: 0.674984053600791      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: 0.674984053600791      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: 0.635331032110145      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: 0.756490658089751      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 ... [28s/37s] OK
• checking PDF version of manual ... [8s/10s] OK
• checking HTML version of manual ... [5s/8s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR